@@ -9,7 +9,7 @@ Authors@R:

             given = "Federico", family = "Marini", role = c("aut", "cre"), 

             email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")

         ),

-		person(

+		    person(

             given = "Annekathrin", family = "Ludt", role = c("aut"), 

             email = "anneludt@uni-mainz.de", comment = c(ORCID = "0000-0002-2475-4945")

         )

@@ -1,5 +1,9 @@

 # GeneTonic 2.2.0

+## New features

+

+* `gs_heatmap` gains the `winsorize_threshold` parameter, to control the behavior of the geneset heatmap in presence of extreme values, either negative or positive ones. If not specified, the heatmap is not introducing any winsorization.

+

 ## Other notes

 * Fixed the behavior of the reactive elements after uploading the `GeneTonicList` object at runtime. 

@@ -28,6 +28,11 @@

 #' specified by [ComplexHeatmap::Heatmap()]

 #' @param center_mean Logical, whether to perform mean centering on the row-wise

 #' @param scale_row Logical, whether to standardize by row the expression values

+#' @param winsorize_threshold Numeric value, to be applied as value to winsorize 

+#' the extreme values of the heatmap. Should be a positive number. Defaults to 

+#' NULL, which corresponds to not applying any winsorization. Suggested values: 

+#' enter 2 or 3 if using row-standardized values (`scale_row` is TRUE), or visually

+#' inspect the range of the values if using simply mean centered values.

 #' @param anno_col_info A character vector of names in `colData(dds)` to use for

 #' decorating the heatmap as annotation.

 #' @param plot_title Character string, to specify the title of the plot,

@@ -95,6 +100,7 @@ gs_heatmap <- function(se,

                        cluster_columns = FALSE,

                        center_mean = TRUE,

                        scale_row = FALSE,

+                       winsorize_threshold = NULL,

                        anno_col_info = NULL,

                        plot_title = NULL,

                        ...) {

@@ -105,6 +111,11 @@ gs_heatmap <- function(se,

     res_enrich <- gtl$res_enrich

     annotation_obj <- gtl$annotation_obj

   }

+  

+  if (!is.null(winsorize_threshold)) {

+    stopifnot(is.numeric(winsorize_threshold))

+    stopifnot(winsorize_threshold >= 0)

+  }

   # check that the data would ideally be a DST, so that it is not the counts/normalized?

   mydata <- assay(se)

@@ -165,6 +176,12 @@ gs_heatmap <- function(se,

     mydata_sig <- mydata_sig[de_to_keep, , drop = FALSE]

   }

+  extreme_value <- max(abs(range(mydata_sig)))

+  if (!is.null(winsorize_threshold)) {

+    # do the winsoring

+    mydata_sig[mydata_sig < -winsorize_threshold] <- -winsorize_threshold

+    mydata_sig[mydata_sig > winsorize_threshold] <- winsorize_threshold

+  } 

   # dim(mydata_sig)

   if (is.null(plot_title)) {

@@ -18,6 +18,7 @@ gs_heatmap(

   cluster_columns = FALSE,

   center_mean = TRUE,

   scale_row = FALSE,

+  winsorize_threshold = NULL,

   anno_col_info = NULL,

   plot_title = NULL,

   ...

@@ -63,6 +64,12 @@ specified by \code{\link[ComplexHeatmap:Heatmap]{ComplexHeatmap::Heatmap()}}}

 \item{scale_row}{Logical, whether to standardize by row the expression values}

+\item{winsorize_threshold}{Numeric value, to be applied as value to winsorize

+the extreme values of the heatmap. Should be a positive number. Defaults to

+NULL, which corresponds to not applying any winsorization. Suggested values:

+enter 2 or 3 if using row-standardized values (\code{scale_row} is TRUE), or visually

+inspect the range of the values if using simply mean centered values.}

+

 \item{anno_col_info}{A character vector of names in \code{colData(dds)} to use for

 decorating the heatmap as annotation.}

@@ -47,6 +47,7 @@ test_that("Geneset heatmap is created", {

     cluster_columns = TRUE,

     center_mean = TRUE,

     scale_row = TRUE,

+    winsorize_threshold = 2,

     anno_col_info = c(

       "condition_char",

       "some_numbers",

@@ -91,6 +92,24 @@ test_that("Geneset heatmap is created", {

       anno_col_info = "condition"

     )

   )

+  

+  expect_error(

+    p5 <- gs_heatmap(

+      se = vst_macrophage,

+      res_de = res_macrophage_IFNg_vs_naive,

+      res_enrich = res_enrich_IFNg_vs_naive,

+      annotation_obj = anno_df,

+      genelist = mycustomlist,

+      FDR = 0.05,

+      de_only = FALSE,

+      cluster_rows = TRUE,

+      cluster_columns = TRUE,

+      center_mean = TRUE,

+      scale_row = TRUE,

+      winsorize_threshold = -3,

+      anno_col_info = "condition"

+    )

+  )

   file.remove("Rplots.pdf")

 })