Merge from documentation

Merge branch 'documentation' into documentation-devel # Conflicts: # DESCRIPTION # vignettes/bivariate.ipynb # vignettes/create_sfe.ipynb # vignettes/create_sfe_v2.ipynb # vignettes/localc.ipynb # vignettes/multispati.ipynb # vignettes/nonspatial.Rmd # vignettes/nonspatial.ipynb # vignettes/preprocess_10xv3.ipynb # vignettes/preprocess_atac.ipynb # vignettes/preprocess_clicktag.ipynb # vignettes/preprocess_crispr.ipynb # vignettes/preprocess_multiome.ipynb # vignettes/preprocess_nuclei.ipynb # vignettes/preprocess_splitseq.ipynb # vignettes/preprocess_visium.ipynb # vignettes/sfemethod.ipynb # vignettes/variogram.ipynb # vignettes/vig10_10x_nuclei.ipynb # vignettes/vig11_clicktags.ipynb # vignettes/vig12_crispr.ipynb # vignettes/vig13_10xatac.ipynb # vignettes/vig14_10xmultiome.ipynb # vignettes/vig1_visium_basic.Rmd # vignettes/vig1_visium_basic.ipynb # vignettes/vig2_visium.Rmd # vignettes/vig2_visium.ipynb # vignettes/vig3_slideseq_v2.ipynb # vignettes/vig4_cosmx.ipynb # vignettes/vig5_xenium.ipynb # vignettes/vig6_merfish.ipynb # vignettes/vig7_seqfish.ipynb # vignettes/vig8_codex.ipynb # vignettes/vig9_splitseq.ipynb # vignettes/visium_10x.ipynb # vignettes/visium_10x_spatial.Rmd # vignettes/visium_10x_spatial.ipynb
pachterlab · Nov 19, 2024 · 51d5674 · 51d5674
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -11,7 +11,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macos-13
+    runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -25,7 +25,7 @@ jobs:
       - name: Setup R and Bioconductor
         uses: grimbough/bioc-actions/setup-bioc@v1
         with:
-          bioc-version: devel
+          bioc-version: release
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: Voyager
 Title: From geospatial to spatial omics
-Version: 1.9.1
+Version: 1.8.1
 Authors@R: 
     c(person("Lambda", "Moses", email = "[email protected]", 
     role = c("aut", "cre"),

diff --git a/R/plot-transcripts.R b/R/plot-transcripts.R
@@ -105,6 +105,7 @@
 #' transcript spots of all genes are plotted.
 #' @param flip Logical, whether to flip the y axis when plotting data from file.
 #' @return A ggplot object, facetting by sample.
+#' @concept Spatial plotting
 #' @export
 #' @importFrom zeallot %<-%
 #' @importFrom SpatialFeatureExperiment .check_rg

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -5,7 +5,7 @@ template:
   bslib:
     text-muted: "#cccccc"
 development:
-  mode: devel
+  mode: auto
 navbar:
   title: "Voyager"
   left:

diff --git a/man/plotTxBin2D.Rd b/man/plotTxBin2D.Rd
diff --git a/vignettes/10xatac_landing.Rmd b/vignettes/10xatac_landing.Rmd
@@ -23,14 +23,14 @@ The vignettes below provide examples of processing raw data using a workflow tha
 
 | Vignette | Colab Notebook | Description |
 |--------------------|:---------------:|---------------------------------|
-| [Preprocess raw data](https://pachterlab.github.io/voyager/dev/articles/preprocess_atac.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/preprocess_atac.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
-| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
+| [Preprocess raw data](https://pachterlab.github.io/voyager/articles/create_mtx_ca.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_mtx_ca.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
+| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
 
 ## Analysis Workflows
 
 The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Google Colab notebooks are linked.
 
 | Vignette          |   Colab Notebook   | Description                   |
   |-------------------|:------------------:|-------------------------------|
-  | [10X ATAC Basic QC](https://pachterlab.github.io/voyager/dev/articles/vig13_10xatac.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/vig13_10xatac.ipynb) | Basic qc and preprocessing |
+  | [10X ATAC Basic QC](https://pachterlab.github.io/voyager/articles/vig13_10xatac.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/vig13_10xatac.ipynb) | Basic qc and preprocessing |
 
diff --git a/vignettes/10xcrispr_landing.Rmd b/vignettes/10xcrispr_landing.Rmd
@@ -24,14 +24,14 @@ The vignettes below provide examples of processing raw data using a workflow tha
 
 | Vignette | Colab Notebook | Description |
 |--------------------|:---------------:|---------------------------------|
-| [Preprocess raw data](https://pachterlab.github.io/voyager/articles/preprocess_crispr.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/preprocess_crispr.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
-| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
+| [Preprocess raw data](https://pachterlab.github.io/voyager/articles/create_mtx_ca.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_mtx_ca.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
+| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
 
 ## Analysis Workflows
 
 The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Colab notebooks are linked.
 
 | Vignette          |   Colab Notebook   | Description                   |
   |-------------------|:------------------:|-------------------------------|
-  | [10X CRISPR Basic QC](https://pachterlab.github.io/voyager/dev/articles/vig12_crispr.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/vig12_crispr.ipynb) | Basic qc and preprocessing |
+  | [10X CRISPR Basic QC](https://pachterlab.github.io/voyager/articles/vig12_crispr.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/vig12_crispr.ipynb) | Basic qc and preprocessing |
 
diff --git a/vignettes/10xmultiome_landing.Rmd b/vignettes/10xmultiome_landing.Rmd
@@ -23,14 +23,14 @@ The vignettes below provide examples of processing raw data using a workflow tha
 
 | Vignette | Colab Notebook | Description |
 |--------------------|:---------------:|---------------------------------|
-| [Preprocess raw data](https://pachterlab.github.io/voyager/dev/articles/preprocess_multiome.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/preprocess_multiome.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
-| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
+| [Preprocess raw data](https://pachterlab.github.io/voyager/articles/create_mtx_ca.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_mtx_ca.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
+| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
 
 ## Analysis Workflows
 
 The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Google Colab notebooks are linked.
 
 | Vignette          |   Colab Notebook   | Description                   |
   |-------------------|:------------------:|-------------------------------|
-  | [10X Multiome Basic QC](https://pachterlab.github.io/voyager/dev/articles/vig14_10xmultiome.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/vig14_10xmultiome.ipynb) | Basic qc and preprocessing |
+  | [10X Multiome Basic QC](https://pachterlab.github.io/voyager/articles/vig14_10xmultiome.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/vig14_10xmultiome.ipynb) | Basic qc and preprocessing |
 
diff --git a/vignettes/10xnuclei_landing.Rmd b/vignettes/10xnuclei_landing.Rmd
@@ -36,14 +36,14 @@ The vignettes below provide examples of processing raw data using a workflow tha
 
 | Vignette | Colab Notebook | Description |
 |--------------------|:---------------:|---------------------------------|
-| [Preprocess raw data](https://pachterlab.github.io/voyager/dev/articles/preprocess_nuclei.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/preprocess_nuclei.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
-| [Create a `SFE` object](https://pachterlab.github.io/voyager/dev/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
+| [Preprocess raw data](https://pachterlab.github.io/voyager/articles/create_mtx_ca.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_mtx_ca.ipynb) | Fetch reference data with `gget`, process raw data with `seqspec`, generate a count matrix with `kallisto-bustools`|
+| [Create a `SFE` object](https://pachterlab.github.io/voyager/articles/create_sfe.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/create_sfe.ipynb) | Download data, create `SFE` object |
 
 ## Analysis Workflows
 
 The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Colab notebooks are linked.
 
 | Vignette          |   Colab Notebook   | Description                   |
   |-------------------|:------------------:|-------------------------------|
-  | [Nuclei Basic QC](https://pachterlab.github.io/voyager/dev/articles/vig10_10x_nuclei.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation-devel/vignettes/vig10_10x_nuclei.ipynb) | Basic qc and preprocessing |
+  | [Nuclei Basic QC](https://pachterlab.github.io/voyager/articles/vig10_10x_nuclei.html) | [Colab Notebook](https://colab.research.google.com/github/pachterlab/voyager/blob/documentation/vignettes/vig10_10x_nuclei.ipynb) | Basic qc and preprocessing |
 
diff --git a/vignettes/bivariate.Rmd b/vignettes/bivariate.Rmd
@@ -91,10 +91,8 @@ if (!file.exists("tissue_lowres_5a.jpeg")) {
 ```
 
 ```{r}
-sfe <- addImg(sfe, file = "tissue_lowres_5a.jpeg", sample_id = "Vis5A", 
-              image_id = "lowres", 
-              scale_fct = 1024/22208)
-sfe <- mirrorImg(sfe, sample_id = "Vis5A", image_id = "lowres")
+sfe <- addImg(sfe, imageSource = "tissue_lowres_5a.jpeg", sample_id = "Vis5A", 
+              image_id = "lowres", scale_fct = 1024/22208)
 ```
 
 ```{r}