merge

Merge remote-tracking branch 'refs/remotes/origin/devel' into devel

# Conflicts:
#	DESCRIPTION
#	R/convenience.R
#	R/processors.R

Author: oganm

.github/workflows/check-bioc.yml

@@ -34,9 +34,9 @@ name: R-CMD-check-bioc
 ## Note that you can always run a GHA test without the cache by using the word
 ## "/nocache" in the commit message.
 env:
-  has_testthat: 'true'
-  run_covr: 'true'
-  run_pkgdown: 'true'
+  has_testthat: 'false'
+  run_covr: 'false'
+  run_pkgdown: 'false'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
   run_docker: 'false'
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
-          - { os: windows-latest, r: '4.4', bioc: '3.19'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -105,16 +105,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-
 
       # - name: Install Linux system dependencies
       #   if: runner.os == 'Linux'
@@ -285,7 +285,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-results
           path: check
 
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gemma.R
 Title: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
-Version: 3.7.3
+Version: 3.9.2
 Authors@R: 
     c(person(given = "Javier", family = "Castillo-Arnemann", 
              role = c("aut"), email = "javiercastilloar@gmail.com",
@@ -26,7 +26,6 @@ URL: https://pavlidislab.github.io/gemma.R/, https://github.com/PavlidisLab/gemm
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
 BugReports: https://github.com/PavlidisLab/gemma.R/issues
 Depends:
     R (>= 4.1.0)
@@ -53,7 +52,8 @@ Imports:
     R.utils,
     kableExtra,
     base64enc,
-    pheatmap
+    pheatmap,
+    grDevices
 Suggests: 
     testthat (>= 2.0.0),
     rmarkdown,
@@ -86,3 +86,4 @@ biocViews:
     Normalization,
     BatchEffect,
     Preprocessing
+Config/roxygen2/version: 8.0.0

R/convenience.R

@@ -733,6 +733,7 @@ get_taxa <- function(memoised = getOption("gemma.memoised", FALSE)){
 #' @param call Gemma API endpoint.
 #' @param ... parameters included in the call
 #' @param json If `TRUE` will parse the content as a list
+#' @param header headers to pass to \code{\link[httr]{add_headers}}
 #' @keywords misc
 #' @return A list if `json = TRUE` and an httr response if `FALSE`
 #' @examples
@@ -1138,11 +1139,13 @@ get_dataset_expression_for_genes <- function(
 #' @param genes An optional list of gene symbols or identifiers
 #' @param adj_p_filter P value threshold to filter genes
 #' @param rank_filter Positive integer or a ratio.
-#' @param ... passed to /code{/link{get_dataset_object}} if dataset is a name
+#' @param ... passed to \code{\link{get_dataset_object}} if dataset is a name
 #' 
 #' @return A list of pheatmap plots for every differential expression contrast of an experiment.
 #' Each plot will be subsetted to exclusively include the relevant subset for the contrast.
 #' 
+#' @keywords dataset
+#' 
 #' @export
 visualize_dataset <- function(dataset,genes = NULL, adj_p_filter = 1, rank_filter = Inf, ...){
     if('character' %in% class(dataset)){
@@ -1202,7 +1205,7 @@ visualize_dataset <- function(dataset,genes = NULL, adj_p_filter = 1, rank_filte
             out <- pheatmap::pheatmap(subset_expression,
                                annotation_col = subset_meta[,!colnames(subset_meta) %in% 'factorValues',drop= FALSE],
                                cluster_cols = FALSE,
-                               cluster_rows = FALSE,
+                               cluster_rows = FALSE,color = viridis::viridis(20),
                                show_colnames = FALSE,scale = 'row',na_col = 'white')
             class(out) = c(class(out),'listable_pheatmap')
             return(out)
@@ -1215,8 +1218,8 @@ visualize_dataset <- function(dataset,genes = NULL, adj_p_filter = 1, rank_filte
 }
 
 #' @export
-print.listable_pheatmap <- function(heatmap){
-    dev.off()
-    heatmap
+print.listable_pheatmap <- function(x, ...){
+    grDevices::dev.off()
+    print(x,...)
 }
 

R/gemma.R.R

@@ -46,4 +46,5 @@ utils::globalVariables(c("platform.ID", "analysis.ID", "analysis.Threshold", "ba
                          "subsetFactor.categoryURI", "subsetFactor.Enabled", "subsetFactor.factorValue", 
                          "subsetFactor.factorValueURI", "valueUri", "category", 
                          "categoryURI", "experimental.factorValue","value",
-                         "contrast.ID","%$%",'baseline.factors',"ID","sample.ID"))
+                         "contrast.ID","%$%",'baseline.factors',"ID","sample.ID","filter_genes","print.listable_pheatmap",
+                         "corrected_pvalue"))

R/subProcessors.R

@@ -11,18 +11,20 @@ read_gzipped_tsv <- function(content){
 
     tmp <- tempfile() # Make a temp file
     writeBin(content, tmp) # Save to that file
-    tmp2 <- gzfile(tmp)
-    ret <- tmp2 %>%
+    con <- gzfile(tmp)
+    
+    lines <- con %>%
         readLines() %>%
-        .[which(!startsWith(., "#"))[1]:length(.)] %>%
-        # Strip comments
-        paste0(collapse = "\n") %>%
-        paste0('\n') %>%
-        {
-            fread(text = .)
-        }
-    close(tmp2)
+        .[which(!startsWith(., "#"))[1]:length(.)]
+    close(con)
+    
+    tmp2 <- tempfile()
+    writeLines(lines,tmp2)
+    
+    ret <- fread(file = tmp2)
+    
     unlink(tmp)
+    unlink(tmp2)
 
     return(ret)
 }