diff --git a/404.html b/404.html index 4d0e3aa..beeb3ed 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
@@ -41,7 +41,7 @@
  • - +
  • @@ -53,7 +53,7 @@
  • @@ -82,7 +82,7 @@
    • - +
    @@ -110,16 +110,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 1e6b3d6..048b42b 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -149,15 +149,15 @@

    Attribution -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index a34f351..2dfff6b 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -85,15 +85,15 @@

    License

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/LICENSE.html b/LICENSE.html index b677c7a..37ccce4 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -89,15 +89,15 @@

    MIT License

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/articles/index.html b/articles/index.html index 3b9188c..ed927b9 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -86,15 +86,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/articles/pcaExplorer.html b/articles/pcaExplorer.html index 76d874d..828d0b6 100644 --- a/articles/pcaExplorer.html +++ b/articles/pcaExplorer.html @@ -14,14 +14,13 @@ - - +
    @@ -44,7 +43,7 @@
  • - +
  • @@ -56,7 +55,7 @@
  • @@ -85,7 +84,7 @@
    • - + @@ -105,9 +104,9 @@

    Harald Binder

    Institute of Medical Biostatistics, Epidemiology and Informatics -(IMBEI), Mainz

    2 May 2024

    +(IMBEI), Mainz

    25 September 2024

    - Source: vignettes/pcaExplorer.Rmd + Source: vignettes/pcaExplorer.Rmd
    @@ -116,7 +115,7 @@

    Harald

    Abstract

    -

    pcaExplorer +

    pcaExplorer provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. Such methods allow for quick information extraction and effective data @@ -126,8 +125,8 @@

    Harald and automated report generation.

    -


    Package: pcaExplorer
    Authors: Federico Marini [aut, cre] (https://orcid.org/0000-0003-3252-7758)
    Version: 2.31.0
    Compiled date: -2024-05-02
    Last edited: 2019-02-26
    License: MIT + file LICENSE

    +


    Package: pcaExplorer
    Authors: Federico Marini [aut, cre] (https://orcid.org/0000-0003-3252-7758)
    Version: 2.99.1
    Compiled date: +2024-09-25
    Last edited: 2019-02-26
    License: MIT + file LICENSE

    +

    +

    Getting started

    -

    pcaExplorer +

    pcaExplorer is an R package distributed as part of the Bioconductor project. To install the package, start R and enter:

     if (!requireNamespace("BiocManager", quietly=TRUE))
     install.packages("BiocManager")
 BiocManager::install("pcaExplorer")
    -

    To install pcaExplorer +

    To install pcaExplorer with all its dependencies (i.e. also the ones listed in the Suggests: field of the DESCRIPTION file, which -include the dataset from the airway +include the dataset from the airway package used as a demo), use this command instead:

     BiocManager::install("pcaExplorer", dependencies = TRUE)
    @@ -170,13 +170,13 @@

    Getting started

    Introduction

    -

    pcaExplorer +

    pcaExplorer is a Bioconductor package containing a Shiny application for analyzing expression data in different conditions and experimental factors.

    It is a general-purpose interactive companion tool for RNA-seq analysis, which guides the user in exploring the Principal Components of the data under inspection.

    -

    pcaExplorer +

    pcaExplorer provides tools and functionality to detect outlier samples, genes that show particular patterns, and additionally provides a functional interpretation of the principal components for further quality @@ -188,48 +188,48 @@

    IntroductionpcaExplorer +

    Starting from development version 1.1.3, pcaExplorer supports reproducible research with state saving and automated report generation. Each generated plot and table can be exported by simple mouse clicks on the dedicated buttons.

    Citation info

    -

    If you use pcaExplorer +

    If you use pcaExplorer for your analysis, please cite it as here below:

     citation("pcaExplorer")
    -
    Please cite the articles below for the 'pcaExplorer' software itself,
-or its usage in combined workflows with the 'ideal' or 'GeneTonic'
-software packages:
-
-  Federico Marini, Harald Binder (2019). pcaExplorer: an R/Bioconductor
-  package for interacting with RNA-seq principal components. BMC
-  Bioinformatics, 20 (1), 331, <doi:10.1186/s12859-019-2879-1>,
-  <doi:10.18129/B9.bioc.pcaExplorer>.
-
-  Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin
-  Strauch, Federico Marini (2022). Interactive and Reproducible
-  Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer,
-  ideal, and GeneTonic. Current Protocols, 2 (4), e411,
-  <doi:10.1002/cpz1.411>.
-
-To see these entries in BibTeX format, use 'print(<citation>,
-bibtex=TRUE)', 'toBibtex(.)', or set
-'options(citation.bibtex.max=999)'.
    +
    #> Please cite the articles below for the 'pcaExplorer' software itself,
+#> or its usage in combined workflows with the 'ideal' or 'GeneTonic'
+#> software packages:
+#> 
+#>   Federico Marini, Harald Binder (2019). pcaExplorer: an R/Bioconductor
+#>   package for interacting with RNA-seq principal components. BMC
+#>   Bioinformatics, 20 (1), 331, <doi:10.1186/s12859-019-2879-1>,
+#>   <doi:10.18129/B9.bioc.pcaExplorer>.
+#> 
+#>   Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin
+#>   Strauch, Federico Marini (2022). Interactive and Reproducible
+#>   Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer,
+#>   ideal, and GeneTonic. Current Protocols, 2 (4), e411,
+#>   <doi:10.1002/cpz1.411>.
+#> 
+#> To see these entries in BibTeX format, use 'print(<citation>,
+#> bibtex=TRUE)', 'toBibtex(.)', or set
+#> 'options(citation.bibtex.max=999)'.

    Launching the application

    -

    After loading the package, the pcaExplorer +

    After loading the package, the pcaExplorer app can be launched in different modes:

    • pcaExplorer(dds = dds, dst = dst), where dds is a DESeqDataSet object and dst is a DESeqTransform object, which were created during an existing session for the analysis of an RNA-seq -dataset with the DESeq2 +dataset with the DESeq2 package.

    • pcaExplorer(dds = dds), where dds is a DESeqDataSet object. The dst object can be @@ -252,7 +252,7 @@

      Launching the application

    Additional parameters and objects that can be provided to the main -pcaExplorer +pcaExplorer function are:

    • pca2go, which is an object created by the @@ -260,10 +260,10 @@

      Launching the applicationpca2go function is based on the -routines and algorithms of the topGO +routines and algorithms of the topGO package, but as an alternative, this object can be computed live during the execution of the app with limmaquickpca2go (which -relies on the goana function provided by the limma +relies on the goana function provided by the limma package). Although this likely provides more general (and probably less informative) functions, it is a good compromise for quickly obtaining a further data interpretation.

      • @@ -282,16 +282,16 @@

      Launching the applicationorg.XX.eg.db packages.

    -

    How to provide your input data in pcaExplorer +

    How to provide your input data in pcaExplorer

    -

    pcaExplorer +

    pcaExplorer supports a number of file formats when uploading the data via the file input widgets. Starting from version 2.9.5, we added functionality to select the separator character for each of the uploadable files. An information box is also shown by clicking on the question mark icon in the Data upload panel, with detailed information (text, as well as screenshots of valid input files) on the format specification.

    -

    In general, pcaExplorer +

    In general, pcaExplorer requires by default tab separated files:

    • the countmatrix: contains the expression matrix, with @@ -311,12 +311,12 @@

      How to provide your input

    -

    Up and running with pcaExplorer +

    Up and running with pcaExplorer

    -

    We recommend users to switch to the dedicated -vignette, entitled “Up and running with pcaExplorer”.

    -

    This document describes a use case for pcaExplorer, -based on the dataset in the airway +

    We recommend users to switch to the dedicated +vignette, entitled “Up and running with pcaExplorer”.

    +

    This document describes a use case for pcaExplorer, +based on the dataset in the airway package.

    @@ -346,7 +346,7 @@

    App settingsThe task menu

    The app panels

    -

    The pcaExplorer +

    The pcaExplorer app is structured in different panels, each focused on a different aspect of the data exploration.

    Most of the panels work extensively with click-based and brush-based @@ -455,7 +455,7 @@

    Data UploadInstructions

    This is where you might be reading a version of the “Up and running -with pcaExplorer” +with pcaExplorer” vignette. Additionally, you can easily reach the fully rendered vignettes, either installed locally, or directly from the Bioconductor package page.

    @@ -627,10 +627,10 @@

    Report Editor

    About

    -

    Contains general information on pcaExplorer, +

    Contains general information on pcaExplorer, including the developer’s contact, the link to the development version in Github, as well as the output of sessionInfo, to use for -reproducibility sake - or bug reporting. Information for citing pcaExplorer +reproducibility sake - or bug reporting. Information for citing pcaExplorer is also reported.

    @@ -639,66 +639,66 @@

    About

    Running pcaExplorer on published datasets

    -

    We can run pcaExplorer +

    We can run pcaExplorer for demonstration purpose on published datasets that are available as SummarizedExperiment in a Bioconductor experiment package.

    -

    We will use the airway +

    We will use the airway dataset, which can be installed with this command:

     if (!requireNamespace("BiocManager", quietly=TRUE))
     install.packages("BiocManager")
 BiocManager::install("airway")
    -

    The airway +

    The airway package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. More details such -as gene models and count quantifications can be found in the airway +as gene models and count quantifications can be found in the airway package vignette.

    -

    The easiest way to explore the airway +

    The easiest way to explore the airway dataset is by clicking on the dedicated button in the Data Upload panel.

    -

    Otherwise, to run pcaExplorer +

    Otherwise, to run pcaExplorer on this dataset from the terminal/RStudio IDE, the following commands are required. First, prepare the objects to be passed as parameters of -pcaExplorer.

    +pcaExplorer.

    -library(airway)
-library(DESeq2)
+library("airway")
+library("DESeq2")
 
-data(airway)
+data("airway", package = "airway")
 
 dds_airway <- DESeqDataSet(airway,design= ~ cell + dex)
 dds_airway
    -
    class: DESeqDataSet 
-dim: 63677 8 
-metadata(2): '' version
-assays(1): counts
-rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
-  ENSG00000273493
-rowData names(10): gene_id gene_name ... seq_coord_system symbol
-colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
-colData names(9): SampleName cell ... Sample BioSample
    +
    #> class: DESeqDataSet 
+#> dim: 63677 8 
+#> metadata(2): '' version
+#> assays(1): counts
+#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
+#>   ENSG00000273493
+#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
+#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
+#> colData names(9): SampleName cell ... Sample BioSample
     rld_airway <- rlogTransformation(dds_airway)
 rld_airway
    -
    class: DESeqTransform 
-dim: 63677 8 
-metadata(2): '' version
-assays(1): ''
-rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
-  ENSG00000273493
-rowData names(17): gene_id gene_name ... dispFit rlogIntercept
-colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
-colData names(10): SampleName cell ... BioSample sizeFactor
    +
    #> class: DESeqTransform 
+#> dim: 63677 8 
+#> metadata(2): '' version
+#> assays(1): ''
+#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
+#>   ENSG00000273493
+#> rowData names(17): gene_id gene_name ... dispFit rlogIntercept
+#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
+#> colData names(10): SampleName cell ... BioSample sizeFactor

    Then launch the app itself.

     pcaExplorer(dds = dds_airway,
             dst = rld_airway)

    The annotation for this dataset can be built by -exploiting the org.Hs.eg.db +exploiting the org.Hs.eg.db package.

     library(org.Hs.eg.db)
@@ -707,13 +707,13 @@ 
    Running pcaExplorer                                row.names = rownames(dds_airway),
                                 stringsAsFactors = FALSE)
 head(annotation_airway)
    -
                    gene_name
-ENSG00000000003    TSPAN6
-ENSG00000000005      TNMD
-ENSG00000000419      DPM1
-ENSG00000000457     SCYL3
-ENSG00000000460     FIRRM
-ENSG00000000938       FGR
    +
    #>                 gene_name
+#> ENSG00000000003    TSPAN6
+#> ENSG00000000005      TNMD
+#> ENSG00000000419      DPM1
+#> ENSG00000000457     SCYL3
+#> ENSG00000000460     FIRRM
+#> ENSG00000000938       FGR

    or alternatively, by using the get_annotation or get_annotation_orgdb wrappers.

    @@ -724,16 +724,16 @@ 
    Running pcaExploreranno_df_biomart <- get_annotation(dds = dds_airway,
                                   biomart_dataset = "hsapiens_gene_ensembl",
                                   idtype = "ensembl_gene_id")
    -
    'select()' returned 1:many mapping between keys and columns
    +
    #> 'select()' returned 1:many mapping between keys and columns
     head(anno_df_orgdb)
    -
                            gene_id gene_name
-ENSG00000000003 ENSG00000000003    TSPAN6
-ENSG00000000005 ENSG00000000005      TNMD
-ENSG00000000419 ENSG00000000419      DPM1
-ENSG00000000457 ENSG00000000457     SCYL3
-ENSG00000000460 ENSG00000000460     FIRRM
-ENSG00000000938 ENSG00000000938       FGR
    +
    #>                         gene_id gene_name
+#> ENSG00000000003 ENSG00000000003    TSPAN6
+#> ENSG00000000005 ENSG00000000005      TNMD
+#> ENSG00000000419 ENSG00000000419      DPM1
+#> ENSG00000000457 ENSG00000000457     SCYL3
+#> ENSG00000000460 ENSG00000000460     FIRRM
+#> ENSG00000000938 ENSG00000000938       FGR

    Then again, the app can be launched with:

     pcaExplorer(dds = dds_airway,
@@ -753,33 +753,33 @@ 
    Running pcaExplorerdds_multifac <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)

    See all the available parameters by typing ?makeExampleDESeqDataSet_multifac. Credits are given to the -initial implementation by Mike Love in the DESeq2 +initial implementation by Mike Love in the DESeq2 package.

    The following steps run the app with the synthetic dataset.

     dds_multifac <- makeExampleDESeqDataSet_multifac(betaSD_condition = 1,betaSD_tissue = 3)
 dds_multifac
    -
    class: DESeqDataSet 
-dim: 1000 12 
-metadata(1): version
-assays(1): counts
-rownames(1000): gene1 gene2 ... gene999 gene1000
-rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
-  trueDisp
-colnames(12): sample1 sample2 ... sample11 sample12
-colData names(2): condition tissue
    +
    #> class: DESeqDataSet 
+#> dim: 1000 12 
+#> metadata(1): version
+#> assays(1): counts
+#> rownames(1000): gene1 gene2 ... gene999 gene1000
+#> rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
+#>   trueDisp
+#> colnames(12): sample1 sample2 ... sample11 sample12
+#> colData names(2): condition tissue
     rld_multifac <- rlogTransformation(dds_multifac)
 rld_multifac
    -
    class: DESeqTransform 
-dim: 1000 12 
-metadata(1): version
-assays(1): ''
-rownames(1000): gene1 gene2 ... gene999 gene1000
-rowData names(11): trueIntercept trueBeta_condition ... dispFit
-  rlogIntercept
-colnames(12): sample1 sample2 ... sample11 sample12
-colData names(3): condition tissue sizeFactor
    +
    #> class: DESeqTransform 
+#> dim: 1000 12 
+#> metadata(1): version
+#> assays(1): ''
+#> rownames(1000): gene1 gene2 ... gene999 gene1000
+#> rowData names(11): trueIntercept trueBeta_condition ... dispFit
+#>   rlogIntercept
+#> colnames(12): sample1 sample2 ... sample11 sample12
+#> colData names(3): condition tissue sizeFactor
     ## checking how the samples cluster on the PCA plot
 pcaplot(rld_multifac,intgroup = c("condition","tissue"))
    @@ -794,7 +794,7 @@

    Running pcaExplorer

    Functions exported by the package for standalone usage

    -

    The functions exported by the pcaExplorer +

    The functions exported by the pcaExplorer package can be also used in a standalone scenario, provided the required objects are in the working environment. They are listed here for an overview, but please refer to the documentation for additional details. @@ -854,16 +854,16 @@

    res_pcairway <- correlatePCs(pcaobj_airway,colData(dds_airway)) res_pcairway

    -
         SampleName       cell        dex albut       Run avgLength Experiment
-PC_1  0.4288799 0.68227033 0.02092134    NA 0.4288799 0.2554109  0.4288799
-PC_2  0.4288799 0.11161023 0.56370286    NA 0.4288799 0.1993592  0.4288799
-PC_3  0.4288799 0.10377716 0.38647623    NA 0.4288799 0.1864725  0.4288799
-PC_4  0.4288799 0.08331631 0.56370286    NA 0.4288799 0.4635148  0.4288799
-        Sample BioSample
-PC_1 0.4288799 0.4288799
-PC_2 0.4288799 0.4288799
-PC_3 0.4288799 0.4288799
-PC_4 0.4288799 0.4288799
    +
    #>      SampleName       cell        dex albut       Run avgLength Experiment
+#> PC_1  0.4288799 0.68227033 0.02092134    NA 0.4288799 0.2554109  0.4288799
+#> PC_2  0.4288799 0.11161023 0.56370286    NA 0.4288799 0.1993592  0.4288799
+#> PC_3  0.4288799 0.10377716 0.38647623    NA 0.4288799 0.1864725  0.4288799
+#> PC_4  0.4288799 0.08331631 0.56370286    NA 0.4288799 0.4635148  0.4288799
+#>         Sample BioSample
+#> PC_1 0.4288799 0.4288799
+#> PC_2 0.4288799 0.4288799
+#> PC_3 0.4288799 0.4288799
+#> PC_4 0.4288799 0.4288799
     plotPCcorrs(res_pcairway)

    @@ -877,48 +877,48 @@ 

     # extract the table of the genes with high loadings
 hi_loadings(pcaobj_airway,topN = 10,exprTable=counts(dds_airway))
    -
                    SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
-ENSG00000143127         11        108         24        485         41
-ENSG00000168309         12        274         35        451          1
-ENSG00000101347       1632      17126       2098      19694       1598
-ENSG00000211445        916      15749       3142      24057       1627
-ENSG00000096060        260       4652        381       3875        601
-ENSG00000163884         70       1325         52        702         36
-ENSG00000171819          4         50         19        543          1
-ENSG00000127954         13        247         25        889          2
-ENSG00000152583         62       2040         99       1172        100
-ENSG00000109906          4        739          5        429          1
-ENSG00000162692        914         62       1192         55       1359
-ENSG00000178695       4746        830       4805        414       5321
-ENSG00000214814        312         24        193         28        501
-ENSG00000164742       1506        347        275         14        137
-ENSG00000138316       1327        207       1521        118       1962
-ENSG00000123610        444        136        303         36       1170
-ENSG00000124766       2483        406       2057        185       2829
-ENSG00000105989        562         47       1575        106        106
-ENSG00000013293        268         23        435         56        558
-ENSG00000146250        330         41        907         89        720
-                SRR1039517 SRR1039520 SRR1039521
-ENSG00000143127        607         77        660
-ENSG00000168309         65          4        193
-ENSG00000101347      17697       1683      32036
-ENSG00000211445      16274       1741      24883
-ENSG00000096060       5493        154       4118
-ENSG00000163884        487         34       1355
-ENSG00000171819         10         14       1067
-ENSG00000127954        199         20        462
-ENSG00000152583       1924         79       2138
-ENSG00000109906        581         12       1113
-ENSG00000162692        171        646         31
-ENSG00000178695       1391       4411        606
-ENSG00000214814         65        789         76
-ENSG00000164742         37        475         56
-ENSG00000138316        618       1045        152
-ENSG00000123610        195        473         37
-ENSG00000124766        870       1851        301
-ENSG00000105989         24        382         46
-ENSG00000013293         75        562         74
-ENSG00000146250        123        439         60
    +
    #>                 SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516
+#> ENSG00000143127         11        108         24        485         41
+#> ENSG00000168309         12        274         35        451          1
+#> ENSG00000101347       1632      17126       2098      19694       1598
+#> ENSG00000211445        916      15749       3142      24057       1627
+#> ENSG00000096060        260       4652        381       3875        601
+#> ENSG00000163884         70       1325         52        702         36
+#> ENSG00000171819          4         50         19        543          1
+#> ENSG00000127954         13        247         25        889          2
+#> ENSG00000152583         62       2040         99       1172        100
+#> ENSG00000109906          4        739          5        429          1
+#> ENSG00000162692        914         62       1192         55       1359
+#> ENSG00000178695       4746        830       4805        414       5321
+#> ENSG00000214814        312         24        193         28        501
+#> ENSG00000164742       1506        347        275         14        137
+#> ENSG00000138316       1327        207       1521        118       1962
+#> ENSG00000123610        444        136        303         36       1170
+#> ENSG00000124766       2483        406       2057        185       2829
+#> ENSG00000105989        562         47       1575        106        106
+#> ENSG00000013293        268         23        435         56        558
+#> ENSG00000146250        330         41        907         89        720
+#>                 SRR1039517 SRR1039520 SRR1039521
+#> ENSG00000143127        607         77        660
+#> ENSG00000168309         65          4        193
+#> ENSG00000101347      17697       1683      32036
+#> ENSG00000211445      16274       1741      24883
+#> ENSG00000096060       5493        154       4118
+#> ENSG00000163884        487         34       1355
+#> ENSG00000171819         10         14       1067
+#> ENSG00000127954        199         20        462
+#> ENSG00000152583       1924         79       2138
+#> ENSG00000109906        581         12       1113
+#> ENSG00000162692        171        646         31
+#> ENSG00000178695       1391       4411        606
+#> ENSG00000214814         65        789         76
+#> ENSG00000164742         37        475         56
+#> ENSG00000138316        618       1045        152
+#> ENSG00000123610        195        473         37
+#> ENSG00000124766        870       1851        301
+#> ENSG00000105989         24        382         46
+#> ENSG00000013293         75        562         74
+#> ENSG00000146250        123        439         60
     # or alternatively plot the values
 hi_loadings(pcaobj_airway,topN = 10,annotation = annotation_airway)
    @@ -962,7 +962,7 @@

    topGOtable is a convenient wrapper for extracting functional GO terms enriched in a subset of genes (such as the differentially expressed genes), based on the algorithm and the -implementation in the topGO +implementation in the topGO package.

     # example not run due to quite long runtime
@@ -995,6 +995,10 @@ 
    
                              ontology = "BP",
                              mapping = "org.Hs.eg.db",
                              geneID = "symbol")
    +

    From version 2.32.0 onwards, the topGOtable() function +has been deprecated, in favor of the equivalent +mosdef::run_topGO() function, which is more robust and +flexible in its usage.

    @@ -1051,27 +1055,27 @@ 

     dds_simu <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 0.5)
 dds_simu
    -
    class: DESeqDataSet 
-dim: 1000 12 
-metadata(1): version
-assays(1): counts
-rownames(1000): gene1 gene2 ... gene999 gene1000
-rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
-  trueDisp
-colnames(12): sample1 sample2 ... sample11 sample12
-colData names(2): condition tissue
    +
    #> class: DESeqDataSet 
+#> dim: 1000 12 
+#> metadata(1): version
+#> assays(1): counts
+#> rownames(1000): gene1 gene2 ... gene999 gene1000
+#> rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
+#>   trueDisp
+#> colnames(12): sample1 sample2 ... sample11 sample12
+#> colData names(2): condition tissue
     dds2_simu <- makeExampleDESeqDataSet_multifac(betaSD_condition = 0.5,betaSD_tissue = 2)
 dds2_simu
    -
    class: DESeqDataSet 
-dim: 1000 12 
-metadata(1): version
-assays(1): counts
-rownames(1000): gene1 gene2 ... gene999 gene1000
-rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
-  trueDisp
-colnames(12): sample1 sample2 ... sample11 sample12
-colData names(2): condition tissue
    +
    #> class: DESeqDataSet 
+#> dim: 1000 12 
+#> metadata(1): version
+#> assays(1): counts
+#> rownames(1000): gene1 gene2 ... gene999 gene1000
+#> rowData names(4): trueIntercept trueBeta_condition trueBeta_tissue
+#>   trueDisp
+#> colnames(12): sample1 sample2 ... sample11 sample12
+#> colData names(2): condition tissue
     rld_simu <- rlogTransformation(dds_simu)
 rld2_simu <- rlogTransformation(dds2_simu)
@@ -1094,7 +1098,7 @@ 
    
 distro_expr(rld_airway,plot_type = "violin")
     distro_expr(rld_airway,plot_type = "boxplot")
    -

    +

    @@ -1107,9 +1111,9 @@

    dst <- DESeq2::rlogTransformation(dds) set.seed(42) geneprofiler(dst,paste0("gene",sample(1:1000,20)), plotZ = FALSE)

    -
    you provided 20 unique identifiers
-20 out of 20 provided genes were found in the data
    -

    +
    #> You provided 20 unique identifiers
    +
    #> 20 out of 20 provided genes were found in the data
    +

    @@ -1121,24 +1125,24 @@

    pcaExplorer function. They use respectively the biomaRt package and the org.XX.eg.db packages.

    -
    +
     anno_df_biomart <- get_annotation(dds = dds_airway,
                                   biomart_dataset = "hsapiens_gene_ensembl",
                                   idtype = "ensembl_gene_id")
    
-
    +
     anno_df_orgdb <- get_annotation_orgdb(dds = dds_airway,
                                       orgdb_species = "org.Hs.eg.db",
                                       idtype = "ENSEMBL")
    
-
    'select()' returned 1:many mapping between keys and columns
    
-
    +
    #> 'select()' returned 1:many mapping between keys and columns
    
+
     head(anno_df_orgdb)
    
-
                            gene_id gene_name
-ENSG00000000003 ENSG00000000003    TSPAN6
-ENSG00000000005 ENSG00000000005      TNMD
-ENSG00000000419 ENSG00000000419      DPM1
-ENSG00000000457 ENSG00000000457     SCYL3
-ENSG00000000460 ENSG00000000460     FIRRM
-ENSG00000000938 ENSG00000000938       FGR
    
+
    #>                         gene_id gene_name
+#> ENSG00000000003 ENSG00000000003    TSPAN6
+#> ENSG00000000005 ENSG00000000005      TNMD
+#> ENSG00000000419 ENSG00000000419      DPM1
+#> ENSG00000000457 ENSG00000000457     SCYL3
+#> ENSG00000000460 ENSG00000000460     FIRRM
+#> ENSG00000000938 ENSG00000000938       FGR
    
 
    If using datasets and annotation packages for yeast samples
 (Saccharomyces cerevisiae, and the org.Sc.sgd.db
 package), remember to specify the key_for_genenames in the
@@ -1151,16 +1155,16 @@ 
    
 
    
 
    Plots the pairwise scatter plots and computes the correlation
 coefficient on the expression matrix provided.
    
-
    +
     # use a subset of the counts to reduce plotting time, it can be time consuming with many samples
 pair_corr(counts(dds_airway)[1:100,])
    
-
    
+
    
 
    
 
    
 
    
 
    Further development
 
    
-
    Additional functionality for the pcaExplorer
+
    Additional functionality for the pcaExplorer
 will be added in the future, as it is tightly related to a topic under
 current development research.
    
 
    Improvements, suggestions, bugs, issues and feedback of any type can
@@ -1169,95 +1173,108 @@ 
    Further development
 
    Session info
 
    
-
    +
-
    R version 4.4.0 (2024-04-24)
-Platform: aarch64-apple-darwin20
-Running under: macOS Sonoma 14.4.1
-
-Matrix products: default
-BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
-LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
-
-locale:
-[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-
-time zone: UTC
-tzcode source: internal
-
-attached base packages:
-[1] stats4    stats     graphics  grDevices utils     datasets  methods  
-[8] base     
-
-other attached packages:
- [1] org.Hs.eg.db_3.19.1         AnnotationDbi_1.65.2       
- [3] DESeq2_1.44.0               airway_1.23.0              
- [5] SummarizedExperiment_1.34.0 GenomicRanges_1.55.4       
- [7] GenomeInfoDb_1.40.0         IRanges_2.38.0             
- [9] S4Vectors_0.42.0            MatrixGenerics_1.16.0      
-[11] matrixStats_1.3.0           pcaExplorer_2.31.0         
-[13] Biobase_2.64.0              BiocGenerics_0.50.0        
-[15] knitr_1.46                  BiocStyle_2.32.0           
-
-loaded via a namespace (and not attached):
-  [1] splines_4.4.0           later_1.3.2             bitops_1.0-7           
-  [4] filelock_1.0.3          tibble_3.2.1            graph_1.82.0           
-  [7] XML_3.99-0.16.1         lifecycle_1.0.4         httr2_1.0.1            
- [10] topGO_2.56.0            doParallel_1.0.17       lattice_0.22-6         
- [13] crosstalk_1.2.1         dendextend_1.17.1       magrittr_2.0.3         
- [16] limma_3.60.0            plotly_4.10.4           sass_0.4.9             
- [19] rmarkdown_2.26.2        jquerylib_0.1.4         yaml_2.3.8             
- [22] shinyBS_0.61.1          httpuv_1.6.15           NMF_0.27               
- [25] DBI_1.2.2               RColorBrewer_1.1-3      abind_1.4-5            
- [28] zlibbioc_1.50.0         purrr_1.0.2             RCurl_1.98-1.14        
- [31] rappdirs_0.3.3          seriation_1.5.5         GenomeInfoDbData_1.2.12
- [34] ggrepel_0.9.5           AnnotationForge_1.46.0  genefilter_1.86.0      
- [37] pheatmap_1.0.12         annotate_1.82.0         pkgdown_2.0.9.9000     
- [40] codetools_0.2-20        DelayedArray_0.30.0     DT_0.33                
- [43] xml2_1.3.6              tidyselect_1.2.1        GOstats_2.70.0         
- [46] farver_2.1.1            UCSC.utils_1.0.0        viridis_0.6.5          
- [49] TSP_1.2-4               BiocFileCache_2.12.0    base64enc_0.1-3        
- [52] webshot_0.5.5           jsonlite_1.8.8          survival_3.6-4         
- [55] iterators_1.0.14        systemfonts_1.0.6       foreach_1.5.2          
- [58] tools_4.4.0             progress_1.2.3          ragg_1.3.0             
- [61] Rcpp_1.0.12             glue_1.7.0              gridExtra_2.3          
- [64] SparseArray_1.4.0       xfun_0.43               dplyr_1.1.4            
- [67] ca_0.71.1               withr_3.0.0             shinydashboard_0.7.2   
- [70] BiocManager_1.30.22     Category_2.70.0         fastmap_1.1.1          
- [73] fansi_1.0.6             SparseM_1.81            digest_0.6.35          
- [76] R6_2.5.1                mime_0.12               textshaping_0.3.7      
- [79] colorspace_2.1-0        GO.db_3.19.1            biomaRt_2.60.0         
- [82] RSQLite_2.3.6           threejs_0.3.3           utf8_1.2.4             
- [85] tidyr_1.3.1             generics_0.1.3          data.table_1.15.4      
- [88] prettyunits_1.2.0       httr_1.4.7              htmlwidgets_1.6.4      
- [91] S4Arrays_1.4.0          pkgconfig_2.0.3         gtable_0.3.5           
- [94] blob_1.2.4              registry_0.5-1          XVector_0.44.0         
- [97] htmltools_0.5.8.1       bookdown_0.39           RBGL_1.80.0            
-[100] GSEABase_1.66.0         scales_1.3.0            png_0.1-8              
-[103] reshape2_1.4.4          curl_5.2.1              shinyAce_0.4.2         
-[106] cachem_1.0.8            stringr_1.5.1           parallel_4.4.0         
-[109] desc_1.4.3              pillar_1.9.0            grid_4.4.0             
-[112] vctrs_0.6.5             promises_1.3.0          dbplyr_2.5.0           
-[115] xtable_1.8-4            cluster_2.1.6           Rgraphviz_2.48.0       
-[118] evaluate_0.23           cli_3.6.2               locfit_1.5-9.9         
-[121] compiler_4.4.0          rlang_1.1.3             crayon_1.5.2           
-[124] rngtools_1.5.2          heatmaply_1.5.0         labeling_0.4.3         
-[127] plyr_1.8.9              fs_1.6.4                stringi_1.8.3          
-[130] viridisLite_0.4.2       gridBase_0.4-7          BiocParallel_1.38.0    
-[133] assertthat_0.2.1        munsell_0.5.1           Biostrings_2.72.0      
-[136] lazyeval_0.2.2          Matrix_1.7-0            hms_1.1.3              
-[139] bit64_4.0.5             ggplot2_3.5.1           KEGGREST_1.44.0        
-[142] statmod_1.5.0           shiny_1.8.1.1           highr_0.10             
-[145] fontawesome_0.5.2       igraph_2.0.3            memoise_2.0.1          
-[148] bslib_0.7.0             bit_4.0.5              
    
+
    #> R version 4.4.1 (2024-06-14)
+#> Platform: aarch64-apple-darwin20
+#> Running under: macOS Sonoma 14.6.1
+#> 
+#> Matrix products: default
+#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
+#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
+#> 
+#> locale:
+#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
+#> 
+#> time zone: UTC
+#> tzcode source: internal
+#> 
+#> attached base packages:
+#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
+#> [8] base     
+#> 
+#> other attached packages:
+#>  [1] org.Hs.eg.db_3.19.1         AnnotationDbi_1.67.0       
+#>  [3] DESeq2_1.45.3               airway_1.25.0              
+#>  [5] SummarizedExperiment_1.35.1 GenomicRanges_1.57.1       
+#>  [7] GenomeInfoDb_1.41.1         IRanges_2.39.2             
+#>  [9] S4Vectors_0.43.2            MatrixGenerics_1.17.0      
+#> [11] matrixStats_1.4.1           pcaExplorer_2.99.1         
+#> [13] Biobase_2.65.1              BiocGenerics_0.51.1        
+#> [15] knitr_1.48                  BiocStyle_2.33.1           
+#> 
+#> loaded via a namespace (and not attached):
+#>   [1] bitops_1.0-8             fs_1.6.4                 enrichplot_1.25.2       
+#>   [4] fontawesome_0.5.2        httr_1.4.7               webshot_0.5.5           
+#>   [7] RColorBrewer_1.1-3       doParallel_1.0.17        Rgraphviz_2.49.0        
+#>  [10] tools_4.4.1              utf8_1.2.4               R6_2.5.1                
+#>  [13] DT_0.33                  mgcv_1.9-1               lazyeval_0.2.2          
+#>  [16] withr_3.0.1              prettyunits_1.2.0        gridExtra_2.3           
+#>  [19] cli_3.6.3                textshaping_0.4.0        TSP_1.2-4               
+#>  [22] scatterpie_0.2.4         labeling_0.4.3           sass_0.4.9              
+#>  [25] topGO_2.57.0             genefilter_1.87.0        goseq_1.57.2            
+#>  [28] pkgdown_2.1.1.9000       Rsamtools_2.21.1         systemfonts_1.1.0       
+#>  [31] yulab.utils_0.1.7        txdbmaker_1.1.1          gson_0.1.0              
+#>  [34] DOSE_3.99.1              R.utils_2.12.3           AnnotationForge_1.47.1  
+#>  [37] limma_3.61.10            RSQLite_2.3.7            GOstats_2.71.0          
+#>  [40] BiocIO_1.15.2            generics_0.1.3           gridGraphics_0.5-1      
+#>  [43] crosstalk_1.2.1          dplyr_1.1.4              dendextend_1.17.1       
+#>  [46] GO.db_3.19.1             Matrix_1.7-0             fansi_1.0.6             
+#>  [49] abind_1.4-8              R.methodsS3_1.8.2        lifecycle_1.0.4         
+#>  [52] yaml_2.3.10              qvalue_2.37.0            SparseArray_1.5.39      
+#>  [55] BiocFileCache_2.13.0     grid_4.4.1               blob_1.2.4              
+#>  [58] promises_1.3.0           crayon_1.5.3             shinydashboard_0.7.2    
+#>  [61] lattice_0.22-6           cowplot_1.1.3            GenomicFeatures_1.57.0  
+#>  [64] annotate_1.83.0          KEGGREST_1.45.1          pillar_1.9.0            
+#>  [67] fgsea_1.31.0             rjson_0.2.23             codetools_0.2-20        
+#>  [70] fastmatch_1.1-4          glue_1.7.0               ggfun_0.1.6             
+#>  [73] data.table_1.16.0        vctrs_0.6.5              png_0.1-8               
+#>  [76] treeio_1.29.1            gtable_0.3.5             assertthat_0.2.1        
+#>  [79] cachem_1.1.0             xfun_0.47                S4Arrays_1.5.8          
+#>  [82] mime_0.12                tidygraph_1.3.1          survival_3.7-0          
+#>  [85] pheatmap_1.0.12          seriation_1.5.6          iterators_1.0.14        
+#>  [88] statmod_1.5.0            Category_2.71.0          nlme_3.1-166            
+#>  [91] ggtree_3.13.1            bit64_4.5.2              threejs_0.3.3           
+#>  [94] progress_1.2.3           filelock_1.0.3           bslib_0.8.0             
+#>  [97] colorspace_2.1-1         DBI_1.2.3                tidyselect_1.2.1        
+#> [100] bit_4.5.0                compiler_4.4.1           curl_5.2.3              
+#> [103] httr2_1.0.4              graph_1.83.0             BiasedUrn_2.0.12        
+#> [106] SparseM_1.84-2           xml2_1.3.6               desc_1.4.3              
+#> [109] DelayedArray_0.31.11     plotly_4.10.4            bookdown_0.40           
+#> [112] shadowtext_0.1.4         rtracklayer_1.65.0       scales_1.3.0            
+#> [115] mosdef_1.1.1             RBGL_1.81.0              NMF_0.28                
+#> [118] rappdirs_0.3.3           stringr_1.5.1            digest_0.6.37           
+#> [121] shinyBS_0.61.1           rmarkdown_2.28           ca_0.71.1               
+#> [124] XVector_0.45.0           htmltools_0.5.8.1        pkgconfig_2.0.3         
+#> [127] base64enc_0.1-3          highr_0.11               dbplyr_2.5.0            
+#> [130] fastmap_1.2.0            rlang_1.1.4              htmlwidgets_1.6.4       
+#> [133] UCSC.utils_1.1.0         shiny_1.9.1              farver_2.1.2            
+#> [136] jquerylib_0.1.4          jsonlite_1.8.9           BiocParallel_1.39.0     
+#> [139] GOSemSim_2.31.2          R.oo_1.26.0              RCurl_1.98-1.16         
+#> [142] magrittr_2.0.3           GenomeInfoDbData_1.2.12  ggplotify_0.1.2         
+#> [145] patchwork_1.3.0          munsell_0.5.1            Rcpp_1.0.13             
+#> [148] ape_5.8                  viridis_0.6.5            stringi_1.8.4           
+#> [151] ggraph_2.2.1             zlibbioc_1.51.1          MASS_7.3-61             
+#> [154] plyr_1.8.9               parallel_4.4.1           ggrepel_0.9.6           
+#> [157] Biostrings_2.73.1        graphlayouts_1.2.0       splines_4.4.1           
+#> [160] hms_1.1.3                geneLenDataBase_1.41.2   locfit_1.5-9.10         
+#> [163] igraph_2.0.3             rngtools_1.5.2           reshape2_1.4.4          
+#> [166] biomaRt_2.61.3           XML_3.99-0.17            evaluate_1.0.0          
+#> [169] BiocManager_1.30.25      foreach_1.5.2            tweenr_2.0.3            
+#> [172] httpuv_1.6.15            tidyr_1.3.1              purrr_1.0.2             
+#> [175] polyclip_1.10-7          heatmaply_1.5.0          ggplot2_3.5.1           
+#> [178] gridBase_0.4-7           ggforce_0.4.2            xtable_1.8-4            
+#> [181] restfulr_0.0.15          tidytree_0.4.6           later_1.3.2             
+#> [184] viridisLite_0.4.2        ragg_1.3.3               tibble_3.2.1            
+#> [187] clusterProfiler_4.13.3   aplot_0.2.3              GenomicAlignments_1.41.0
+#> [190] memoise_2.0.1            registry_0.5-1           cluster_2.1.6           
+#> [193] GSEABase_1.67.0          shinyAce_0.4.2
    
 
    
   
    
 
   
+
    @@ -1270,16 +1287,16 @@

    Session info

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/articles/pcaExplorer_files/figure-html/unnamed-chunk-10-1.png b/articles/pcaExplorer_files/figure-html/unnamed-chunk-11-1.png similarity index 100% rename from articles/pcaExplorer_files/figure-html/unnamed-chunk-10-1.png rename to articles/pcaExplorer_files/figure-html/unnamed-chunk-11-1.png diff --git a/articles/pcaExplorer_files/figure-html/unnamed-chunk-6-1.png b/articles/pcaExplorer_files/figure-html/unnamed-chunk-6-1.png deleted file mode 100644 index eed4619..0000000 Binary files a/articles/pcaExplorer_files/figure-html/unnamed-chunk-6-1.png and /dev/null differ diff --git a/articles/pcaExplorer_files/figure-html/unnamed-chunk-7-1.png b/articles/pcaExplorer_files/figure-html/unnamed-chunk-7-1.png index a7611f3..05c1d81 100644 Binary files a/articles/pcaExplorer_files/figure-html/unnamed-chunk-7-1.png and b/articles/pcaExplorer_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/pcaExplorer_files/figure-html/unnamed-chunk-8-1.png b/articles/pcaExplorer_files/figure-html/unnamed-chunk-8-1.png new file mode 100644 index 0000000..a7611f3 Binary files /dev/null and b/articles/pcaExplorer_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/upandrunning.html b/articles/upandrunning.html index 0b6f2f4..29a937a 100644 --- a/articles/upandrunning.html +++ b/articles/upandrunning.html @@ -13,14 +13,13 @@ - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -55,7 +54,7 @@
  • @@ -84,13 +83,13 @@
    • - +

    -

    Up and running with pcaExplorer

    +

    Up and running with pcaExplorer

    Federico Marini

    @@ -102,9 +101,9 @@

    Harald Binder

    Institute of Medical Biostatistics, Epidemiology and Informatics -(IMBEI), Mainz

    2 May 2024

    +(IMBEI), Mainz

    25 September 2024

    - Source: vignettes/upandrunning.Rmd + Source: vignettes/upandrunning.Rmd
    @@ -127,14 +126,14 @@

    Harald

    Setup

    -

    First things first: install pcaExplorer +

    First things first: install pcaExplorer and load it into your R session. You should receive a message notification if this is completed without errors.

     BiocManager::install("pcaExplorer")
 library("pcaExplorer")
    -

    This document describes a use case for pcaExplorer, -based on the dataset in the airway +

    This document describes a use case for pcaExplorer, +based on the dataset in the airway package. If this package is not available on your machine, please install it by executing:

    @@ -151,22 +150,22 @@ 
    Start exploring - the bea
 
-
    The easiest way to explore the airway
+
    The easiest way to explore the airway
 dataset is by clicking on the dedicated button in the Data
 Upload panel. This action will:
    
 
      
-
    • load the airway
+
    • load the airway
 package
      • 
 
    • load the count matrix and the experimental metadata
      • 
 
    • compose the dds object, normalize the expression values
 (using the robust method proposed by Anders and Huber in the original
 DESeq manuscript), and compute the variance stabilizing transformed
 expression values (stored in the dst object)
      • 
-
    • retrieve the gene annotation information via the org.Hs.eg.db,
+
    • retrieve the gene annotation information via the org.Hs.eg.db,
 adding gene symbols to the ENSEMBL ids - this step is optional, but
 recommended for more human-readable identifiers to be used.
      • 
 
    
-
    If you want to load your expression data, please refer to the User
+
    If you want to load your expression data, please refer to the User
 Guide, which contains detailed information on the formats your data
 have to respect.
    
 
    Once the preprocessing of the input is done, you should get a
@@ -361,12 +360,12 @@ 
    Start exploring - the bea

    Still, a previous call to pca2go is recommended, as it -relies on the algorithm of the topGO +relies on the algorithm of the topGO package: it will require some additional computing time, but it is likely to deliver more precise terms (i.e. in turn more relevant from the point of view of their biological relevance). To do so, you should exit the live session, compute this object, and provide it in the call -to pcaExplorer (see more how to do so in the +to pcaExplorer (see more how to do so in the main user guide).

    @@ -430,9 +429,9 @@

    Session Info -
    ## R version 4.4.0 (2024-04-24)
+
    ## R version 4.4.1 (2024-06-14)
 ## Platform: aarch64-apple-darwin20
-## Running under: macOS Sonoma 14.4.1
+## Running under: macOS Sonoma 14.6.1
 ## 
 ## Matrix products: default
 ## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
@@ -448,29 +447,25 @@ 
    Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] BiocStyle_2.32.0
+## [1] BiocStyle_2.33.1
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.46         
-##  [4] rlang_1.1.3         xfun_0.43           highr_0.10         
-##  [7] png_0.1-8           purrr_1.0.2         textshaping_0.3.7  
-## [10] jsonlite_1.8.8      htmltools_0.5.8.1   ragg_1.3.0         
-## [13] sass_0.4.9          rmarkdown_2.26.2    evaluate_0.23      
-## [16] jquerylib_0.1.4     fastmap_1.1.1       yaml_2.3.8         
-## [19] lifecycle_1.0.4     memoise_2.0.1       bookdown_0.39      
-## [22] BiocManager_1.30.22 compiler_4.4.0      fs_1.6.4           
-## [25] htmlwidgets_1.6.4   systemfonts_1.0.6   digest_0.6.35      
-## [28] R6_2.5.1            magrittr_2.0.3      bslib_0.7.0        
-## [31] tools_4.4.0         pkgdown_2.0.9.9000  cachem_1.0.8       
-## [34] desc_1.4.3
    
+##  [1] cli_3.6.3           knitr_1.48          rlang_1.1.4        
+##  [4] xfun_0.47           highr_0.11          png_0.1-8          
+##  [7] textshaping_0.4.0   jsonlite_1.8.9      htmltools_0.5.8.1  
+## [10] ragg_1.3.3          sass_0.4.9          rmarkdown_2.28     
+## [13] evaluate_1.0.0      jquerylib_0.1.4     fastmap_1.2.0      
+## [16] yaml_2.3.10         lifecycle_1.0.4     bookdown_0.40      
+## [19] BiocManager_1.30.25 compiler_4.4.1      fs_1.6.4           
+## [22] htmlwidgets_1.6.4   systemfonts_1.1.0   digest_0.6.37      
+## [25] R6_2.5.1            bslib_0.8.0         tools_4.4.1        
+## [28] pkgdown_2.1.1.9000  cachem_1.1.0        desc_1.4.3

    +
    @@ -483,16 +478,16 @@

    Session Info

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/authors.html b/authors.html index 816f503..e77a4c4 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -67,7 +67,7 @@

    Authors and Citation

    - +
    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/index.html b/index.html index cfc22fa..28d5f6c 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • - +
  • @@ -54,7 +54,7 @@
  • @@ -83,7 +83,7 @@
    • - +
    @@ -233,16 +233,16 @@

    Developers

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/news/index.html b/news/index.html index f9f3010..61e8d36 100644 --- a/news/index.html +++ b/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    +
    +

    pcaExplorer 2.99.0

    +
    +

    New features

    +
    • The pcaplot() function now provides a clever default for the intgroup parameter, if some content (as it should) is provided in the colData slot of the main input object
      • +
    +
    +

    Other notes

    +
    • The transition to the functions available in the mosdef Bioconductor is complete, with the original functions now being deprecated. This applies to topGOtable() (now replaced by mosdef::run_topGO())
      • +
    • The gene plot widgets now also use the gene_plot() function from mosdef, instead of the previous undocumented internal function
      • +
    • The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
      • +
    • Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level
      • +
    +

    pcaExplorer 2.22.0

    @@ -389,15 +403,15 @@

    New features
    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/pkgdown.yml b/pkgdown.yml index c05cfbd..ca752dd 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,8 +1,7 @@ pandoc: 3.1.11 -pkgdown: 2.0.9.9000 -pkgdown_sha: 9a6bbfc6ecf3aaf94406783beb0154fec0f3e87c +pkgdown: 2.1.1.9000 +pkgdown_sha: 0a18bc718640aee7160a0ebbcdef5ecaae2ac4a4 articles: pcaExplorer: pcaExplorer.html upandrunning: upandrunning.html -last_built: 2024-05-02T15:22Z - +last_built: 2024-09-25T17:54Z diff --git a/reference/Rplot001.png b/reference/Rplot001.png deleted file mode 100644 index 17a3580..0000000 Binary files a/reference/Rplot001.png and /dev/null differ diff --git a/reference/Rplot002.png b/reference/Rplot002.png deleted file mode 100644 index 81a3049..0000000 Binary files a/reference/Rplot002.png and /dev/null differ diff --git a/reference/correlatePCs.html b/reference/correlatePCs.html index 12cc2b4..e018c22 100644 --- a/reference/correlatePCs.html +++ b/reference/correlatePCs.html @@ -6,7 +6,7 @@ - +
    @@ -28,7 +28,7 @@
    - +

    Principal components (cor)relation with experimental covariates

    - Source: R/correlatePCs.R + Source: R/correlatePCs.R
    @@ -84,7 +84,9 @@

    Principal components (cor)relation with experimental covariates

    Arguments

    -
    pcaobj
    + + +
    pcaobj

    A prcomp object

    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    A data.frame object with computed p values for each covariate +

    A data.frame object with computed p values for each covariate and for each principal component

    @@ -175,15 +175,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/deprecated.html b/reference/deprecated.html new file mode 100644 index 0000000..515579e --- /dev/null +++ b/reference/deprecated.html @@ -0,0 +1,138 @@ + +Deprecated functions in pcaExplorer — deprecated • pcaExplorer + + +
    +
    + + + +
    +
    +
    +

    Deprecated functions in pcaExplorer

    + Source: R/deprecated.R + +
    + +
    +

    Functions that are on their way to the function afterlife. +Their successors are also listed.

    +
    + + +
    +

    Arguments

    + + +
    ...
    +

    Ignored arguments.

    + +
    +
    +

    Value

    +

    All functions throw a warning, with a deprecation message pointing +towards its descendent (if available).

    +
    +
    +

    Details

    +

    The successors of these functions are likely coming after the rework that +led to the creation of the mosdef package. See more into its +documentation for more details.

    +
    +
    +

    Transitioning to the mosdef framework

    + + +
    +
    +

    Author

    +

    Federico Marini

    +
    + +
    +

    Examples

    + 
    # try(topGOtable())
+
+
    +
    +
    + +
    + + +
    + + + + + + + + diff --git a/reference/distro_expr-1.png b/reference/distro_expr-1.png index 551696b..c1a8e65 100644 Binary files a/reference/distro_expr-1.png and b/reference/distro_expr-1.png differ diff --git a/reference/distro_expr.html b/reference/distro_expr.html index 8ae6c22..14e342f 100644 --- a/reference/distro_expr.html +++ b/reference/distro_expr.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Plot distribution of expression values

    - Source: R/distro_expr.R + Source: R/distro_expr.R
    @@ -78,8 +78,10 @@

    Plot distribution of expression values

    Arguments

    -
    rld
    -

    A DESeqTransform object.

    + + +
    rld
    +

    A DESeqTransform() object.

    plot_type
    @@ -89,9 +91,7 @@

    Arguments

    Value

    - - -

    A plot with the distribution of the expression values

    +

    A plot with the distribution of the expression values

    @@ -114,15 +114,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/geneprofiler.html b/reference/geneprofiler.html index 2c20ef7..d08ab49 100644 --- a/reference/geneprofiler.html +++ b/reference/geneprofiler.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Extract and plot the expression profile of genes

    - Source: R/profile_explore.R + Source: R/profile_explore.R
    @@ -78,9 +78,11 @@

    Extract and plot the expression profile of genes

    Arguments

    -
    se
    -

    A DESeqDataSet object, or a -DESeqTransform object.

    + + +
    se
    +

    A DESeqDataSet() object, or a +DESeqTransform() object.

    genelist
    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    A plot of the expression profile for the genes

    +

    A plot of the expression profile for the genes

    @@ -109,12 +109,12 @@

    Examples

    dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
 rlt <- DESeq2::rlogTransformation(dds)
 geneprofiler(rlt, paste0("gene", sample(1:1000, 20)))
-#> you provided 20 unique identifiers
-#> 20 out of 20 provided genes were found in the data
+#> You provided 20 unique identifiers
+#> 20 out of 20 provided genes were found in the data
 
 geneprofiler(rlt, paste0("gene", sample(1:1000, 20)), plotZ = TRUE)
-#> you provided 20 unique identifiers
-#> 20 out of 20 provided genes were found in the data
+#> You provided 20 unique identifiers
+#> 20 out of 20 provided genes were found in the data
    @@ -130,15 +130,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/genespca-1.png b/reference/genespca-1.png index 81bf3ed..15c7e79 100644 Binary files a/reference/genespca-1.png and b/reference/genespca-1.png differ diff --git a/reference/genespca-2.png b/reference/genespca-2.png index e22940e..751a250 100644 Binary files a/reference/genespca-2.png and b/reference/genespca-2.png differ diff --git a/reference/genespca.html b/reference/genespca.html index 284b463..72f1525 100644 --- a/reference/genespca.html +++ b/reference/genespca.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Principal components analysis on the genes

    - Source: R/genespca.R + Source: R/genespca.R
    @@ -109,10 +109,12 @@

    Principal components analysis on the genes

    Arguments

    -
    x
    -

    A DESeqTransform object, with data in assay(x), -produced for example by either rlog or -varianceStabilizingTransformation

    + + +
    x
    +

    A DESeqTransform() object, with data in assay(x), +produced for example by either rlog() or +varianceStabilizingTransformation()

    ntop
    @@ -199,7 +201,7 @@

    Arguments

    varname.adjust

    Adjustment factor the placement of the variable names, ->= 1 means farther from the arrow

    +'>= 1' means farther from the arrow

    varname.abbrev
    @@ -236,9 +238,7 @@

    Arguments

    Value

    - - -

    An object created by ggplot, which can be assigned and further customized.

    +

    An object created by ggplot, which can be assigned and further customized.

    Details

    @@ -280,15 +280,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/get_annotation.html b/reference/get_annotation.html index 9dcaa22..6d074c4 100644 --- a/reference/get_annotation.html +++ b/reference/get_annotation.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Get an annotation data frame from biomaRt

    - Source: R/get_annotation.R + Source: R/get_annotation.R
    @@ -78,8 +78,10 @@

    Get an annotation data frame from biomaRt

    Arguments

    -
    dds
    -

    A DESeqDataSet object

    + + +
    dds
    +

    A DESeqDataSet() object

    biomart_dataset
    @@ -89,20 +91,18 @@

    Arguments

    idtype

    Character, the ID type of the genes as in the row names of -dds, to be used for the call to getBM

    +dds, to be used for the call to getBM()

    Value

    - - -

    A data frame for ready use in pcaExplorer, retrieved from biomaRt.

    +

    A data frame for ready use in pcaExplorer, retrieved from biomaRt.

    Examples

    - 
    library(airway)
-data(airway)
+    
    library("airway")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -116,9 +116,9 @@ 
    Examples
    
 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                              colData = colData(airway),
                                              design = ~dex+cell)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 get_annotation(dds_airway, "hsapiens_gene_ensembl", "ensembl_gene_id")
-}
+} # }
    @@ -133,15 +133,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/get_annotation_orgdb.html b/reference/get_annotation_orgdb.html index 1af92fb..bd76385 100644 --- a/reference/get_annotation_orgdb.html +++ b/reference/get_annotation_orgdb.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Get an annotation data frame from org db packages

    - Source: R/get_annotation.R + Source: R/get_annotation.R
    @@ -78,8 +78,10 @@

    Get an annotation data frame from org db packages

    Arguments

    -
    dds
    -

    A DESeqDataSet object

    + + +
    dds
    +

    A DESeqDataSet() object

    orgdb_species
    @@ -89,29 +91,27 @@

    Arguments

    idtype

    Character, the ID type of the genes as in the row names of -dds, to be used for the call to mapIds

    +dds, to be used for the call to mapIds()

    key_for_genenames
    -

    Character, corresponding to the column name for the -key in the orgDb package containing the official gene name (often called -gene symbol). +

    Character, corresponding to the column name for the +key in the orgDb package containing the official gene name (often called +gene symbol). This parameter defaults to "SYMBOL", but can be adjusted in case the key is not found in the annotation package (e.g. for org.Sc.sgd.db).

    Value

    - - -

    A data frame for ready use in pcaExplorer, retrieved from the +

    A data frame for ready use in pcaExplorer, retrieved from the org db packages

    Examples

    - 
    library(airway)
-data(airway)
+    
    library("airway")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -152,15 +152,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.9000.
    
+  
    Site built with pkgdown 2.1.1.9000.
    - - + + diff --git a/reference/hi_loadings.html b/reference/hi_loadings.html index 33d85de..93da3d5 100644 --- a/reference/hi_loadings.html +++ b/reference/hi_loadings.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Extract genes with highest loadings

    - Source: R/hi_loadings.R + Source: R/hi_loadings.R
    @@ -85,7 +85,9 @@

    Extract genes with highest loadings

    Arguments

    -
    pcaobj
    + + +
    pcaobj

    A prcomp object

    @@ -99,7 +101,7 @@

    Arguments

    exprTable
    -

    A matrix object, e.g. the counts of a DESeqDataSet. +

    A matrix object, e.g. the counts of a DESeqDataSet(). If not NULL, returns the counts matrix for the selected genes

    @@ -114,9 +116,7 @@

    Arguments

    Value

    - - -

    A ggplot2 object, or a matrix, if exprTable is not null

    +

    A ggplot2 object, or a matrix, if exprTable is not null

    @@ -194,15 +194,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/index.html b/reference/index.html index ffdd08f..6a809fc 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • pcaExplorerPackage index • pcaExplorer - +
    @@ -25,7 +25,7 @@
    - +
    @@ -154,6 +154,14 @@

    Expression data exploration makeExampleDESeqDataSet_multifac()

    Make a simulated DESeqDataSet for two or more experimental factors

    + +

    Deprecated functions in pcaExplorer

    +

    + + +

    deprecated

    + +

    Deprecated functions in pcaExplorer

    - - + + diff --git a/reference/limmaquickpca2go.html b/reference/limmaquickpca2go.html index bcef377..4fcc30f 100644 --- a/reference/limmaquickpca2go.html +++ b/reference/limmaquickpca2go.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Functional interpretation of the principal components, based on simple overrepresentation analysis

    - Source: R/pca2go.R + Source: R/pca2go.R
    @@ -91,10 +91,12 @@

    Functional interpretation of the principal components, based on simple overr

    Arguments

    -
    se
    -

    A DESeqTransform object, with data in assay(se), -produced for example by either rlog or -varianceStabilizingTransformation

    + + +
    se
    +

    A DESeqTransform() object, with data in assay(se), +produced for example by either rlog() or +varianceStabilizingTransformation()

    pca_ngenes
    @@ -129,18 +131,16 @@

    Arguments

    Value

    - - -

    A nested list object containing for each principal component the terms enriched +

    A nested list object containing for each principal component the terms enriched in each direction. This object is to be thought in combination with the displaying feature -of the main pcaExplorer function

    +of the main pcaExplorer() function

    Examples

    - 
    library(airway)
-library(DESeq2)
-library(limma)
+    
    library("airway")
+library("DESeq2")
+library("limma")
 #> 
 #> Attaching package: ‘limma’
 #> The following object is masked from ‘package:DESeq2’:
@@ -149,7 +149,7 @@ 
    Examples
    
 #> The following object is masked from ‘package:BiocGenerics’:
 #> 
 #>     plotMA
-data(airway)
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -161,13 +161,13 @@ 
    Examples
    
 #> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
 #> colData names(9): SampleName cell ... Sample BioSample
 dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 rld_airway <- rlogTransformation(dds_airway)
 goquick_airway <- limmaquickpca2go(rld_airway,
                                    pca_ngenes = 10000,
                                    inputType = "ENSEMBL",
                                    organism = "Hs")
-}
+} # }
    @@ -183,15 +183,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/makeExampleDESeqDataSet_multifac.html b/reference/makeExampleDESeqDataSet_multifac.html index 5553fa3..4f4e3de 100644 --- a/reference/makeExampleDESeqDataSet_multifac.html +++ b/reference/makeExampleDESeqDataSet_multifac.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Make a simulated DESeqDataSet for two or more experimental factors

    - Source: R/makeds.R + Source: R/makeds.R
    @@ -91,7 +91,9 @@

    Make a simulated DESeqDataSet for two or more experimental factors

    Arguments

    -
    n
    + + +
    n

    number of rows (genes)

    @@ -126,16 +128,14 @@

    Arguments

    Value

    - - -

    a DESeqDataSet with true dispersion, +

    a DESeqDataSet() with true dispersion, intercept for two factors (condition and tissue) and beta values in the - metadata columns. Note that the true betas are provided on the log2 scale.

    +metadata columns. Note that the true betas are provided on the log2 scale.

    Details

    This function is designed and inspired following the proposal of -makeExampleDESeqDataSet from the DESeq2 package. Credits are given +makeExampleDESeqDataSet() from the DESeq2 package. Credits are given to Mike Love for the nice initial implementation

    @@ -178,15 +178,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pair_corr-1.png b/reference/pair_corr-1.png index f92801e..776b178 100644 Binary files a/reference/pair_corr-1.png and b/reference/pair_corr-1.png differ diff --git a/reference/pair_corr.html b/reference/pair_corr.html index 8a9c8c7..b3baec0 100644 --- a/reference/pair_corr.html +++ b/reference/pair_corr.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Pairwise scatter and correlation plot of counts

    - Source: R/pair_corr.R + Source: R/pair_corr.R
    @@ -78,7 +78,9 @@

    Pairwise scatter and correlation plot of counts

    Arguments

    -
    df
    + + +
    df

    A data frame, containing the (raw/normalized/transformed) counts

    @@ -99,15 +101,13 @@

    Arguments

    Value

    - - -

    A plot with pairwise scatter plots and correlation coefficients

    +

    A plot with pairwise scatter plots and correlation coefficients

    Examples

    - 
    library(airway)
-data(airway)
+    
    library("airway")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -122,34 +122,6 @@ 
    Examples
    
                                              colData = colData(airway),
                                              design = ~dex+cell)
 pair_corr(counts(dds_airway)[1:100, ]) # use just a subset for the example
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
-#> Warning: argument 1 does not name a graphical parameter
    @@ -165,15 +137,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pca2go.html b/reference/pca2go.html index 3266f1d..e67fec4 100644 --- a/reference/pca2go.html +++ b/reference/pca2go.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    Functional interpretation of the principal components

    - Source: R/pca2go.R + Source: R/pca2go.R
    @@ -95,10 +95,12 @@

    Functional interpretation of the principal components

    Arguments

    -
    se
    -

    A DESeqTransform object, with data in assay(se), -produced for example by either rlog or -varianceStabilizingTransformation

    + + +
    se
    +

    A DESeqTransform() object, with data in assay(se), +produced for example by either rlog() or +varianceStabilizingTransformation()

    pca_ngenes
    @@ -141,7 +143,7 @@

    Arguments

    annopkg
    -

    String containing the name of the organism annotation package. Can be used to +

    String containing the name of the organism annotation package. Can be used to override the organism parameter, e.g. in case of alternative identifiers used in the annotation package (Arabidopsis with TAIR)

    @@ -152,18 +154,16 @@

    Arguments

    Value

    - - -

    A nested list object containing for each principal component the terms enriched +

    A nested list object containing for each principal component the terms enriched in each direction. This object is to be thought in combination with the displaying feature -of the main pcaExplorer function

    +of the main pcaExplorer() function

    Examples

    - 
    library(airway)
-library(DESeq2)
-data(airway)
+    
    library("airway")
+library("DESeq2")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -175,7 +175,7 @@ 
    Examples
    
 #> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
 #> colData names(9): SampleName cell ... Sample BioSample
 dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 rld_airway <- rlogTransformation(dds_airway)
 # constructing the annotation object
 anno_df <- data.frame(gene_id = rownames(dds_airway),
@@ -195,7 +195,7 @@ 
    Examples
    
                         organism = "Hs",
                         ensToGeneSymbol = TRUE,
                         background_genes = bg_ids)
-}
+} # }
    @@ -211,15 +211,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pcaExplorer-pkg.html b/reference/pcaExplorer-pkg.html index 9cf8880..754017e 100644 --- a/reference/pcaExplorer-pkg.html +++ b/reference/pcaExplorer-pkg.html @@ -5,7 +5,7 @@ - +
    @@ -27,7 +27,7 @@
    - +

    pcaExplorer: analyzing time-lapse microscopy imaging, from detection to tracking

    - Source: R/pcaExplorer-pkg.R + Source: R/pcaExplorer-pkg.R
    @@ -108,15 +108,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pcaExplorer.html b/reference/pcaExplorer.html index 709ab4c..6f7910f 100644 --- a/reference/pcaExplorer.html +++ b/reference/pcaExplorer.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Explore a dataset from a PCA perspective

    - Source: R/pcaExplorer.R + Source: R/pcaExplorer.R
    @@ -88,14 +88,16 @@

    Explore a dataset from a PCA perspective

    Arguments

    -
    dds
    -

    A DESeqDataSet object. If not provided, then a countmatrix + + +

    dds
    +

    A DESeqDataSet() object. If not provided, then a countmatrix and a coldata need to be provided. If none of the above is provided, it is possible to upload the data during the execution of the Shiny App

    dst
    -

    A DESeqTransform object. Can be computed from the dds object +

    A DESeqTransform() object. Can be computed from the dds object if left NULL. If none is provided, then a countmatrix and a coldata need to be provided. If none of the above is provided, it is possible to upload the data during the execution of the Shiny App

    @@ -112,7 +114,7 @@

    Arguments

    pca2go
    -

    An object generated by the pca2go function, which contains +

    An object generated by the pca2go() function, which contains the information on enriched functional categories in the genes that show the top or bottom loadings in each principal component of interest. If not provided, it is possible to compute live during the execution of the Shiny App

    @@ -129,15 +131,13 @@

    Arguments

    Value

    - - -

    A Shiny App is launched for interactive data exploration

    +

    A Shiny App is launched for interactive data exploration

    Examples

    - 
    library(airway)
-data(airway)
+    
    library("airway")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -151,7 +151,7 @@ 
    Examples
    
 dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                              colData = colData(airway),
                                              design = ~dex+cell)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 rld_airway <- DESeq2::rlogTransformation(dds_airway)
 
 pcaExplorer(dds_airway, rld_airway)
@@ -159,7 +159,7 @@ 
    Examples
    
 pcaExplorer(countmatrix = counts(dds_airway), coldata = colData(dds_airway))
 
 pcaExplorer() # and then upload count matrix, covariate matrix (and eventual annotation)
-}
+} # }
    @@ -175,15 +175,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pcaplot-1.png b/reference/pcaplot-1.png index 3fdb75a..c278af8 100644 Binary files a/reference/pcaplot-1.png and b/reference/pcaplot-1.png differ diff --git a/reference/pcaplot.html b/reference/pcaplot.html index 9139af4..907401b 100644 --- a/reference/pcaplot.html +++ b/reference/pcaplot.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Sample PCA plot for transformed data

    - Source: R/pcaplot.R + Source: R/pcaplot.R
    @@ -75,7 +75,7 @@

    Sample PCA plot for transformed data

    pcaplot(
   x,
-  intgroup = "condition",
+  intgroup = NULL,
   ntop = 500,
   returnData = FALSE,
   title = NULL,
@@ -90,15 +90,18 @@ 
    Sample PCA plot for transformed data
    
 
     
    
     
    Arguments
    
-    
    x
    
-
    A DESeqTransform object, with data in assay(x),
-produced for example by either rlog or
-varianceStabilizingTransformation
    
+
+
+
    x
    
+
    A DESeqTransform() object, with data in assay(x),
+produced for example by either rlog() or
+varianceStabilizingTransformation()/vst()
    
 
 
 
    intgroup
    
 
    Interesting groups: a character vector of
-names in colData(x) to use for grouping
    
+names in colData(x) to use for grouping. Defaults to NULL, which would then
+select the first column of the colData slot
    
 
 
 
    ntop
    
@@ -141,9 +144,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An object created by ggplot, which can be assigned and further customized.
    
+    
    An object created by ggplot, which can be assigned and further customized.
    
     
    
 
     
    
@@ -151,6 +152,7 @@ 
    Examples
    
     
    dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
 rlt <- DESeq2::rlogTransformation(dds)
 pcaplot(rlt, ntop = 200)
+#> Defaulting to 'condition' as the `intgroup` parameter...
 
 
 
    
@@ -167,15 +169,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.9000.
    
+  
    Site built with pkgdown 2.1.1.9000.
    - - + + diff --git a/reference/pcaplot3d.html b/reference/pcaplot3d.html index a4b7774..72c1765 100644 --- a/reference/pcaplot3d.html +++ b/reference/pcaplot3d.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Sample PCA plot for transformed data

    - Source: R/pcaplot.R + Source: R/pcaplot.R
    @@ -89,10 +89,12 @@

    Sample PCA plot for transformed data

    Arguments

    -
    x
    -

    A DESeqTransform object, with data in assay(x), -produced for example by either rlog or -varianceStabilizingTransformation

    + + +
    x
    +

    A DESeqTransform() object, with data in assay(x), +produced for example by either rlog() or +varianceStabilizingTransformation()

    intgroup
    @@ -136,9 +138,7 @@

    Arguments

    Value

    - - -

    A html-based visualization of the 3d PCA plot

    +

    A html-based visualization of the 3d PCA plot

    @@ -161,15 +161,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/pcascree-1.png b/reference/pcascree-1.png index 201cf99..45ffbd6 100644 Binary files a/reference/pcascree-1.png and b/reference/pcascree-1.png differ diff --git a/reference/pcascree-2.png b/reference/pcascree-2.png index 67762c6..6c18aef 100644 Binary files a/reference/pcascree-2.png and b/reference/pcascree-2.png differ diff --git a/reference/pcascree.html b/reference/pcascree.html index fa00bb2..1dee0b0 100644 --- a/reference/pcascree.html +++ b/reference/pcascree.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Scree plot of the PCA on the samples

    - Source: R/pcaplot.R + Source: R/pcaplot.R
    @@ -80,7 +80,9 @@

    Scree plot of the PCA on the samples

    Arguments

    -
    obj
    + + +
    obj

    A prcomp object

    @@ -99,9 +101,7 @@

    Arguments

    Value

    - - -

    An object created by ggplot, which can be assigned and further customized.

    +

    An object created by ggplot, which can be assigned and further customized.

    @@ -128,15 +128,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/plotPCcorrs.html b/reference/plotPCcorrs.html index 2a8246f..bbc3e68 100644 --- a/reference/plotPCcorrs.html +++ b/reference/plotPCcorrs.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Plot significance of (cor)relations of covariates VS principal components

    - Source: R/correlatePCs.R + Source: R/correlatePCs.R
    @@ -78,7 +78,9 @@

    Plot significance of (cor)relations of covariates VS principal components

    Arguments

    -
    pccorrs
    + + +
    pccorrs

    A data.frame object generated by correlatePCs

    @@ -94,9 +96,7 @@

    Arguments

    Value

    - - -

    A base plot object

    +

    A base plot object

    @@ -123,15 +123,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/reference/topGOtable.html b/reference/topGOtable.html index 1361847..9a1c80e 100644 --- a/reference/topGOtable.html +++ b/reference/topGOtable.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Extract functional terms enriched in the DE genes, based on topGO

    - Source: R/pca2go.R + Source: R/pca2go.R
    @@ -96,7 +96,9 @@

    Extract functional terms enriched in the DE genes, based on topGO

    Arguments

    -
    DEgenes
    + + +
    DEgenes

    A vector of (differentially expressed) genes

    @@ -155,30 +157,28 @@

    Arguments

    do_padj

    Logical, whether to perform the adjustment on the p-values from the specific -topGO method, based on the FDR correction. Defaults to FALSE, since the assumption of +topGO method, based on the FDR correction. Defaults to FALSE, since the assumption of independent hypotheses is somewhat violated by the intrinsic DAG-structure of the Gene Ontology Terms

    Value

    - - -

    A table containing the computed GO Terms and related enrichment scores

    +

    A table containing the computed GO Terms and related enrichment scores

    Details

    Allowed values assumed by the topGO_method2 parameter are one of the -following: elim, weight, weight01, lea, -parentchild. For more details on this, please refer to the original +following: elim, weight, weight01, lea, +parentchild. For more details on this, please refer to the original documentation of the topGO package itself

    Examples

    - 
    library(airway)
-library(DESeq2)
-data(airway)
+    
    library("airway")
+library("DESeq2")
+data("airway", package = "airway")
 airway
 #> class: RangedSummarizedExperiment 
 #> dim: 63677 8 
@@ -192,7 +192,7 @@ 
    Examples
    
 dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)
 # Example, performing extraction of enriched functional categories in
 # detected significantly expressed genes
-if (FALSE) {
+if (FALSE) { # \dontrun{
 dds_airway <- DESeq(dds_airway)
 res_airway <- results(dds_airway)
 library("AnnotationDbi")
@@ -221,7 +221,7 @@ 
    Examples
    
                              ontology = "BP",
                              mapping = "org.Hs.eg.db",
                              geneID = "symbol")
-}
+} # }
    @@ -237,15 +237,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.9000.

    +

    Site built with pkgdown 2.1.1.9000.

    - - + + diff --git a/sitemap.xml b/sitemap.xml index c745afc..4a6b7ee 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,90 +1,33 @@ - - - - /404.html - - - /CODE_OF_CONDUCT.html - - - /LICENSE-text.html - - - /LICENSE.html - - - /articles/index.html - - - /articles/pcaExplorer.html - - - /articles/upandrunning.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/correlatePCs.html - - - /reference/distro_expr.html - - - /reference/geneprofiler.html - - - /reference/genespca.html - - - /reference/get_annotation.html - - - /reference/get_annotation_orgdb.html - - - /reference/hi_loadings.html - - - /reference/index.html - - - /reference/limmaquickpca2go.html - - - /reference/makeExampleDESeqDataSet_multifac.html - - - /reference/pair_corr.html - - - /reference/pca2go.html - - - /reference/pcaExplorer-pkg.html - - - /reference/pcaExplorer.html - - - /reference/pcaplot.html - - - /reference/pcaplot3d.html - - - /reference/pcascree.html - - - /reference/plotPCcorrs.html - - - /reference/topGOtable.html - + +/404.html +/CODE_OF_CONDUCT.html +/LICENSE-text.html +/LICENSE.html +/articles/index.html +/articles/pcaExplorer.html +/articles/upandrunning.html +/authors.html +/index.html +/news/index.html +/reference/correlatePCs.html +/reference/deprecated.html +/reference/distro_expr.html +/reference/geneprofiler.html +/reference/genespca.html +/reference/get_annotation.html +/reference/get_annotation_orgdb.html +/reference/hi_loadings.html +/reference/index.html +/reference/limmaquickpca2go.html +/reference/makeExampleDESeqDataSet_multifac.html +/reference/pair_corr.html +/reference/pca2go.html +/reference/pcaExplorer-pkg.html +/reference/pcaExplorer.html +/reference/pcaplot.html +/reference/pcaplot3d.html +/reference/pcascree.html +/reference/plotPCcorrs.html +/reference/topGOtable.html +