Adding the functionality to enable limma and edgeR objects

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

@@ -57,7 +57,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows' && matrix.config.image == null
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}

NAMESPACE

@@ -53,6 +53,7 @@ importFrom(clusterProfiler,enrichGO)
 importFrom(ggforce,geom_sina)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_point)
@@ -64,6 +65,7 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,position_jitter)
+importFrom(ggplot2,rel)
 importFrom(ggplot2,scale_color_discrete)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_colour_manual)
@@ -72,6 +74,7 @@ importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,scale_y_log10)
 importFrom(ggplot2,stat_summary)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,xlab)

R/color_mgmt.R

@@ -189,19 +189,39 @@ de_table_painter <- function(res_de,
                              ) {
   ## Checks on the input parameters
 
-  res_de <- res_de[order(res_de$padj), ]
-  my_dt <- DT::datatable(
-    as.data.frame(res_de),
-    escape = FALSE,
-    options = list(
-      scrollX = TRUE,
-      scrollY = "400px",
-      pageLength = 25,
-      columnDefs = list(
-        list(className = "dt-center", targets = "_all")
+  if (is(res_de, "DESeqResults")) {
+    res_de <- res_de[order(res_de$padj), ]
+    my_dt <- DT::datatable(
+      as.data.frame(res_de),
+      escape = FALSE,
+      options = list(
+        scrollX = TRUE,
+        scrollY = "400px",
+        pageLength = 25,
+        columnDefs = list(
+          list(className = "dt-center", targets = "_all")
+        )
       )
     )
-  )
+  } else if ((is(res_de, "DGELRT")) | (is(res_de, "DGEEXACT"))) {
+    # TODO: any conversion
+    # TODO: possibly also re-change the default values of the column names where to find things in
+    message("Working with edgeR objects, remove me later")
+  } else {
+    res_de <- res_de[order(res_de$padj), ]
+    my_dt <- DT::datatable(
+      as.data.frame(res_de),
+      escape = FALSE,
+      options = list(
+        scrollX = TRUE,
+        scrollY = "400px",
+        pageLength = 25,
+        columnDefs = list(
+          list(className = "dt-center", targets = "_all")
+        )
+      )
+    )
+  }
 
   if (!is.null(rounding_digits)) {
     my_dt <- formatRound(

R/de2df.R

@@ -39,3 +39,14 @@ deresult_to_df <- function(res_de, FDR = NULL) {
   }
   res
 }
+
+.deresult_to_df.DESeq <- function() {
+
+}
+
+.deresult_to_df.edgeR <- function() {
+
+}
+
+
+

R/expression_summaries.R

@@ -71,6 +71,3 @@ pair_corr <- function(df, log = TRUE, method = "pearson", use_subset = TRUE) {
         xlim = c(rangeMin, rangeMax),
         ylim = c(rangeMin, rangeMax))
 }
-
-
-## couple more TODO

R/gene_annotation.R

@@ -38,6 +38,15 @@ get_annotation_orgdb <- function(de_container,
                                  orgdb_package,
                                  id_type,
                                  key_for_genenames = "SYMBOL") {
+
+  ## TODO: see if we need any checks
+  if (is(de_container, "DESeqDataSet")) {
+    ## TODO
+    # all we need is rownames
+  }
+
+
+
   if (is.null(orgdb_package))
     stop("Select an annotation package to generate the corresponding annotation")