version bump

HelenaLC · Feb 27, 2024 · 3680824 · 3680824
2 parents 3bbb17f + 026566e
commit 3680824
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.18'}
-          - { os: windows-latest, r: 'devel', bioc: '3.18'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
+          - { os: windows-latest, r: 'devel', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CATALYST
 Type: Package
 Title: Cytometry dATa anALYSis Tools
-Version: 1.27.0
-Depends: R (>= 4.2), SingleCellExperiment
+Version: 1.27.1
+Depends: R (>= 4.4), SingleCellExperiment
 Authors@R: c(
 	person("Helena L.", "Crowell", 
 	    role=c("aut", "cre"),

diff --git a/NEWS b/NEWS
@@ -1,3 +1,14 @@
+changes in version 1.27.1
+
++ bug fix in 'plotDiffHeatmap': add 'drop=FALSE'
+  to avoid failure for DA when 1 cluster remains
+
++ fix typos in differential vignette (issue #387)
+
+changes in version 1.27.0
+
++ Bioconductor release 3.18
+
 changes in version 1.25.1
 
 + fixed unit tests for differential plotting
@@ -6,7 +17,7 @@ changes in version 1.25.1
 
 changes in version 1.25.0
 
-+ Bioconductor release 3.18
++ Bioconductor release 3.17
 
 changes in version 1.23.5
 

diff --git a/R/plotDiffHeatmap.R b/R/plotDiffHeatmap.R
@@ -243,7 +243,7 @@ plotDiffHeatmap <- function(x, y, k = NULL,
         da = {
             ns <- table(x$cluster_id, x$sample_id)
             fq <- prop.table(ns, 2)
-            fq <- fq[top$cluster_id, ]
+            fq <- fq[top$cluster_id, , drop=FALSE]
             y <- as.matrix(unclass(fq))
             if (normalize) y <- .z_normalize(asin(sqrt(y)))
             Heatmap(

diff --git a/tests/testthat/test_plotDiffHeatmap.R b/tests/testthat/test_plotDiffHeatmap.R
@@ -68,6 +68,12 @@ test_that("plotDiffHeatmap() - DA; cluster filtering", {
     }
 })
 
+test_that("plotDiffHeatmap() - DA; single cluster (#382)", {
+    y <- da[da$cluster_id == 1, ]
+    p <- plotDiffHeatmap(x, y)
+    expect_is(p, "Heatmap")
+})
+
 test_that("plotDiffHeatmap() - DS; cluster filtering", {
     for (ks in lapply(c(1, 3, 5), sample, x = levels(kids))) {
         y <- filterSCE(x, !cluster_id %in% ks, k = k)

diff --git a/vignettes/differential.Rmd b/vignettes/differential.Rmd
@@ -26,8 +26,6 @@ output:
 knitr::opts_chunk$set(cache = TRUE)
 ```
 
----
-
 <span style="color:firebrick">**Most of the pipeline and visualizations presented herein have been adapted from @Nowicka2019-F1000's *"CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets"* available [here](https://f1000research.com/articles/6-748/v4).**</span>
 
 ```{r warning = FALSE, message = FALSE}
@@ -121,10 +119,10 @@ sce <- cluster(sce, features = "type",
 
 Let K = `xdim` x `ydim` be the number of `r BiocStyle::Biocpkg("FlowSOM")` clusters. `cluster` will add information to the following slots of the input `SingleCellExperiment`: 
 
-- `rowData`:
-  - `cluster_id`: cluster ID as inferred by `r BiocStyle::Biocpkg("FlowSOM")`. One of 1, ..., K.
+- `rowData``:
+  - `marker_class`: factor `"type"` or `"state"`. Specifies whether a marker has been used for clustering or not, respectively.
 - `colData`:
-  - `marker_class`: factor `"type"` or `"state"`. Specifyies whether a marker has been used for clustering or not, respectively.
+  - `cluster_id`: cluster ID as inferred by `r BiocStyle::Biocpkg("FlowSOM")`. One of 1, ..., K.
 - `metadata`:
   - `SOM_codes`: a table with dimensions K x (# type markers). Contains the SOM codes. 
   - `cluster_codes`: a table with dimensions K x (`maxK` + 1). Contains the cluster codes for all metaclusterings.

diff --git a/vignettes/preprocessing.Rmd b/vignettes/preprocessing.Rmd
@@ -39,8 +39,6 @@ output:
 knitr::opts_chunk$set(cache = TRUE)
 ```
 
----
-
 <span style="color:firebrick">**Most of the pipeline and visualizations presented herein have been adapted from @Chevrier2018-CATALYST's *"Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry"* available [here](https://doi.org/10.1016/j.cels.2018.02.010).**</span>
 
 ```{r load-libs, warning = FALSE, message = FALSE}
-Original file line number
+Diff line change
@@ Expand Up / @@ -39,8 +39,6 @@ output: @@
     knitr::opts_chunk$set(cache = TRUE)
     ```
-    ---
     <span style="color:firebrick">**Most of the pipeline and visualizations presented herein have been adapted from @Chevrier2018-CATALYST's *"Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry"* available [here](https://doi.org/10.1016/j.cels.2018.02.010).**</span>
     ```{r load-libs, warning = FALSE, message = FALSE}
@@ Expand Down @@