Merge pull request #469 from ncborcherding/dev

v2.3.2

.github/workflows/R-CMD-check.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pr-commands.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scRepertoire
 Title: A toolkit for single-cell immune receptor profiling
-Version: 2.2.1
+Version: 2.3.2
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "[email protected]"), 
     person(given = "Qile", family = "Yang", role = c("aut"), email = "[email protected]"), 
@@ -25,7 +25,6 @@ Imports:
     grDevices,
     igraph,
     iNEXT,
-    methods,
     plyr,
     quantreg,
     Rcpp,
@@ -35,17 +34,15 @@ Imports:
     S4Vectors,
     SeuratObject,
     SingleCellExperiment,
-    stats,
     stringr,
     stringdist,
     SummarizedExperiment,
     tidygraph,
     truncdist,
-    utils,
     VGAM,
-    hash,
     purrr,
-    lifecycle
+    lifecycle,
+    methods
 Suggests: 
     BiocManager,
     BiocStyle,
@@ -57,7 +54,8 @@ Suggests:
     Seurat,
     spelling,
     testthat (>= 3.0.0),
-    vdiffr
+    vdiffr,
+    withr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Language: en-US

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 Nick Borcherding
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: scRepertoire authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 scRepertoire authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,5 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(quietBCRgenes,Seurat)
+S3method(quietBCRgenes,default)
+S3method(quietTCRgenes,Seurat)
+S3method(quietTCRgenes,default)
 export(StartracDiversity)
 export(addVariable)
 export(alluvialClones)
@@ -24,8 +28,10 @@ export(combineExpression)
 export(combineTCR)
 export(createHTOContigList)
 export(exportClones)
+export(expression2List)
 export(getCirclize)
 export(getContigDoublets)
+export(getHumanIgPseudoGenes)
 export(highlightClones)
 export(loadContigs)
 export(percentAA)
@@ -34,6 +40,9 @@ export(percentKmer)
 export(percentVJ)
 export(positionalEntropy)
 export(positionalProperty)
+export(quietBCRgenes)
+export(quietTCRgenes)
+export(quietVDJgenes)
 export(subsetClones)
 export(vizGenes)
 import(ggplot2)

NEWS.md

@@ -1,6 +1,18 @@
+# scRepertoire VERSION 2.3.2
+
+## UNDERLYING CHANGES
+* Fixed issue with denominator in ```getCirclize()```
+
 # scRepertoire VERSION 2.2.1
 
-#VERSION BUMP FOR BIOCONDUCTOR
+* Rebasing for the purposes of Bioconductor version 2.2.0
+
+## NEW FEATURES
+* Added support for BCRs for loading ParseBio sequences.
+* Added `quietBCRgenes()` and `quietTCRgenes()` from Ibex and Trex and `quietVDJgenes()` as a convenience that runs both. The functions filter out known TCR and/or BCR gene signatures.
+
+## UNDERLYING CHANGES
+* Added `Seurat` to the `Suggests` field in the DESCRIPTION file.
 
 # scRepertoire VERSION 2.0.8
 

R/alluvialClones.R

@@ -62,11 +62,9 @@
 #' environment in addition to the visualization.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals].
-#' 
-#' @import ggplot2
+#'
 #' @importFrom ggalluvial StatStratum geom_flow geom_stratum to_lodes_form geom_alluvium
-#' @importFrom dplyr %>% mutate
-#' 
+#'
 #' @export
 #' @concept SC_Functions
 #' @return Alluvial ggplot comparing clone distribution.

R/clonalBias.R

@@ -43,9 +43,7 @@
 #' @param exportTable Returns the data frame used for forming the graph.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals].
-#' @import ggplot2
 #' @importFrom quantreg rqss
-#' @importFrom stringr str_sort
 #' @export
 #' @concept SC_Functions
 #' @return ggplot scatter plot with clone bias

R/clonalCluster.R

@@ -37,8 +37,7 @@
 #' @importFrom stringdist stringdist
 #' @importFrom igraph set_vertex_attr V union
 #' @importFrom plyr join
-#' @importFrom dplyr bind_rows summarize
-#' @importFrom stringr str_split str_replace_all
+#' @importFrom stringr str_replace_all
 #' @importFrom rlang %||%
 #' @importFrom SummarizedExperiment colData<- colData
 #' @importFrom stats na.omit

R/clonalCompare.R

@@ -47,10 +47,6 @@
 #' @param exportTable Returns the data frame used for forming the graph
 #' @param palette Colors to use in visualization - input any
 #' \link[grDevices]{hcl.pals}
-
-#' @import ggplot2
-#' @importFrom stringr str_sort
-#'
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the proportion of total sequencing read of

R/clonalDiversity.R

@@ -67,10 +67,8 @@
 #' @param return.boots export boot strapped values calculated - 
 #' will automatically exportTable = TRUE.
 #' @param skip.boots remove down sampling and boot strapping from the calculation.
-#' @importFrom stringr str_sort str_split
-#' @importFrom reshape2 melt
+#'
 #' @importFrom dplyr sample_n
-#' @import ggplot2
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the diversity of clones by group

R/clonalHomeostasis.R

@@ -30,10 +30,7 @@
 #' environment in addition to the visualization.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals].
-#' @import ggplot2
-#' @importFrom stringr str_split
-#' @importFrom reshape2 melt
-#' @importFrom dplyr bind_rows
+#'
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the space occupied by the specific proportion of clones

R/clonalLength.R

@@ -29,11 +29,9 @@
 #' @param exportTable Returns the data frame used for forming the graph.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals]
-#' @importFrom stringr str_split
-#' @importFrom ggplot2 ggplot
 #' @export
 #' @concept Visualizing_Clones
-#' @return ggplot of the discrete or relative length distributions of 
+#' @return ggplot of the discrete or relative length distributions of
 #' clone sequences
 clonalLength <- function(input.data, 
                          cloneCall = "aa", 

R/clonalNetwork.R

@@ -48,13 +48,10 @@
 #' @param exportClones Exports a table of clones that are shared
 #' across multiple identity groups and ordered by the total number
 #' of clone copies.
-#' @param palette Colors to use in visualization - input any 
+#' @param palette Colors to use in visualization - input any
 #' [hcl.pals][grDevices::hcl.pals].
-
-#' @import ggplot2
-#' @importFrom stringr str_sort
 #' @importFrom igraph graph_from_data_frame V `V<-`
-#' @importFrom dplyr %>% group_by select summarize_all count n across all_of desc
+#' @importFrom dplyr summarize_all count across all_of desc
 #' @importFrom tidygraph as_tbl_graph activate
 #' @importFrom ggraph ggraph geom_edge_bend  geom_node_point scale_edge_colour_gradientn circle guide_edge_colourbar
 #' @importFrom stats setNames

R/clonalOccupy.R

@@ -35,9 +35,7 @@
 #' environment in addition to the visualization
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals]
-#' @importFrom dplyr %>% group_by mutate count
-#' @importFrom reshape2 melt
-#' @import ggplot2
+#' @importFrom dplyr count
 #' @export
 #' @concept SC_Functions
 #' @return Stacked bar plot of counts of cells by clone frequency group

R/clonalOverlap.R

@@ -56,8 +56,7 @@
 #' @param exportTable Returns the data frame used for forming the graph
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals]
-#' @importFrom stringr str_sort str_to_title
-#' @importFrom reshape2 melt
+#' @importFrom stringr str_to_title
 #' @importFrom stats quantile
 #' @export
 #' @concept Visualizing_Clones

R/clonalOverlay.R

@@ -31,8 +31,7 @@
 #' cut.category variable in the meta data of the single-cell object.
 #' @param bins The number of contours to the overlay
 #' @param facet.by meta data variable to facet the comparison
-#' 
-#' @import ggplot2
+#'
 #' @importFrom SeuratObject Embeddings
 #' @export
 #' @concept SC_Functions

R/clonalProportion.R

@@ -31,11 +31,6 @@
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals]
 #'
-#' @import ggplot2
-#' @importFrom stringr str_sort
-#' @importFrom reshape2 melt
-#' @importFrom dplyr bind_rows n
-#'
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the space occupied by the specific rank of clones

R/clonalQuant.R

@@ -28,7 +28,6 @@
 #' @param exportTable Returns the data frame used for forming the graph
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals]
-#' @import ggplot2
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the total or relative unique clones

R/clonalRarefaction.R

@@ -37,9 +37,8 @@
 #' environment in addition to the visualization.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals].
-#' 
+#'
 #' @importFrom iNEXT iNEXT ggiNEXT
-#' @import ggplot2
 #' @export
 #' @concept Visualizing_Clones
 clonalRarefaction <- function(input.data,

R/clonalScatter.R

@@ -32,9 +32,7 @@
 #' @param exportTable Returns the data frame used for forming the graph.
 #' @param palette Colors to use in visualization - input any 
 #' [hcl.pals][grDevices::hcl.pals].
-#' 
-#' @import ggplot2
-#' 
+#'
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot of the relative clone numbers between two sequencing runs or groups

R/clonalSizeDistribution.R

@@ -30,35 +30,34 @@
 #' 
 #' @examples
 #' #Making combined contig data
-#' combined <- combineTCR(contig_list, 
-#'                         samples = c("P17B", "P17L", "P18B", "P18L", 
+#' combined <- combineTCR(contig_list,
+#'                         samples = c("P17B", "P17L", "P18B", "P18L",
 #'                                     "P19B","P19L", "P20B", "P20L"))
 #' clonalSizeDistribution(combined, cloneCall = "strict", method="ward.D2")
 #'
-#' @param input.data The product of [combineTCR()], 
+#' @param input.data The product of [combineTCR()],
 #' [combineBCR()], or [combineExpression()].
-#' @param cloneCall How to call the clone - VDJC gene (**gene**), 
+#' @param cloneCall How to call the clone - VDJC gene (**gene**),
 #' CDR3 nucleotide (**nt**), CDR3 amino acid (**aa**),
-#' VDJC gene + CDR3 nucleotide (**strict**) or a custom variable 
-#' in the data. 
-#' @param chain indicate if both or a specific chain should be used - 
+#' VDJC gene + CDR3 nucleotide (**strict**) or a custom variable
+#' in the data.
+#' @param chain indicate if both or a specific chain should be used -
 #' e.g. "both", "TRA", "TRG", "IGH", "IGL".
-#' @param threshold Numerical vector containing the thresholds 
+#' @param threshold Numerical vector containing the thresholds
 #' the grid search was performed over.
 #' @param method The clustering parameter for the dendrogram.
 #' @param group.by The variable to use for grouping.
 #' @param exportTable Returns the data frame used for forming the graph.
-#' @param palette Colors to use in visualization - input any 
+#' @param palette Colors to use in visualization - input any
 #' [hcl.pals][grDevices::hcl.pals].
-#' @import ggplot2 
-#' @importFrom dplyr bind_rows
+#'
 #' @importFrom ggdendro dendro_data segment label
 #' @importFrom stats hclust optim pgamma as.dist
 #' @export
 #' @concept Visualizing_Clones
 #' @return ggplot dendrogram of the clone size distribution
 #' @author Hillary Koch
-
+#'
 clonalSizeDistribution <- function(input.data,
                                    cloneCall ="strict", 
                                    chain = "both",