@@ -1,7 +1,7 @@

 Package: pipeComp

 Type: Package

 Title: pipeComp pipeline benchmarking framework

-Version: 0.99.34

+Version: 0.99.35

 Depends: R (>= 4.0)

 Authors@R: c(

 	person("Pierre-Luc", "Germain", email="[email protected]", role=c("cre","aut"), comment = c(ORCID = "0000-0003-3418-4218")), 

@@ -34,10 +34,11 @@

 #' aggregation) can be passed.

 #' @param show_heatmap_legend Passed to `Heatmap` (default FALSE)

 #' @param show_column_names Passed to `Heatmap` (default FALSE)

-#' @param col Colors for the heatmap. By default, will apply linear mapping (if

+#' @param col Colors for the heatmap, or a color-mapping function as produced by

+#' `colorRamp2`. If passing a vector of colors and the data is scaled, there 

+#' should be an odd number of colors. By default, will apply linear mapping (if

 #' the data is not scaled) or signed sqrt mapping (if scaled) on the 

-#' `viridisLite::inferno` palette. To disable the signed sqrt-transformation,

-#' simply pass `col=viridisLite::inferno(100)` or your own palette.

+#' `viridisLite::inferno` palette.

 #' @param font_factor A scaling factor applied to fontsizes (default 1)

 #' @param value_cols A vector of length 2 indicating the colors of the values

 #' (above and below the mean), if printed

@@ -121,7 +122,8 @@ evalHeatmap <- function( res, step=NULL, what, what2=NULL, agg.by=NULL,

   res2 <- .doscale(res, param=scale)

   ro <- .dosort(res2, reorder_rows)

   res2 <- as.matrix(res2)

-  cellfn <- .getCellFn(res, res2, value_format, value_cols, font_factor)

+  cellfn <- .getCellFn(res, res2, value_format, value_cols, font_factor, 

+                       scaled=!(is.logical(scale) && !scale) )

   if(is.null(title)) title <- gsub("\\.","\n",what)

   suppressWarnings({

     if(!tryCatch(is.null(row_split), error=function(e) FALSE)){

@@ -138,8 +140,9 @@ evalHeatmap <- function( res, step=NULL, what, what2=NULL, agg.by=NULL,

     }

   })

   if(is.null(name)) name <- what

-  if(is.null(col))

-    col <- .defaultColorMapping(res2, center=!(is.logical(scale) && !scale))

+  if(is.null(col) || !is.function(col))

+    col <- .defaultColorMapping(res2, center=!(is.logical(scale) && !scale),

+                                cols=col)

   Heatmap( res2, name=name, cluster_rows=FALSE, cluster_columns=FALSE, 

            show_heatmap_legend=show_heatmap_legend, row_order=ro,

            bottom_annotation=.ds_anno(colnames(res),anno_legend,font_factor), 

@@ -148,7 +151,7 @@ evalHeatmap <- function( res, step=NULL, what, what2=NULL, agg.by=NULL,

            row_title_gp = gpar(fontsize = (14*font_factor)),

            column_title_gp = gpar(fontsize = (14*font_factor)),

            row_names_gp = gpar(fontsize = (12*font_factor)),

-           column_names_gp = gpar(fontsize = (12*font_factor)), ...)

+           column_names_gp = gpar(fontsize = (12*font_factor)), ... )

 }

 .doscale <- function(res, param){

@@ -194,12 +197,13 @@ evalHeatmap <- function( res, step=NULL, what, what2=NULL, agg.by=NULL,

   rep(0,length(x))

 }

-.defaultColorMapping <- function(x, center=TRUE){

-  if(!center) return(viridisLite::inferno(101))

+.defaultColorMapping <- function(x, center=TRUE, cols=NULL){

+  if(is.null(cols)) cols <- viridisLite::inferno(101)

+  if(!center) return(cols)

   q <- max(abs(range(x, na.rm=TRUE)))

-  b <- c( -seq(from=sqrt(q), to=0, length.out=51)^2,

-          seq(from=0, to=sqrt(q), length.out=51)[-1]^2 )

-  colorRamp2(b, viridisLite::inferno(101))

+  b <- c( -seq(from=sqrt(q), to=0, length.out=floor(length(cols)/2)+1)^2,

+          seq(from=0, to=sqrt(q), length.out=floor(length(cols)/2)+1)[-1]^2 )

+  colorRamp2(b, cols)

 }

 #' colCenterScale

@@ -302,9 +306,14 @@ colCenterScale <- function(x, centerFn=median,

 #' @importFrom grid grid.text

 .getCellFn  <- function( res, res2, value_format, cols=c("black","white"), 

-                         font_factor=1 ){

-  resmid <- range(res2, na.rm=TRUE)

-  resmid <- resmid[1]+(resmid[2]-resmid[1])/2

+                         font_factor=1, scaled=TRUE ){

+  if(scaled){

+    resmid <- median(res2, na.rm=TRUE)

+  }else{

+    resmid <- range(res2, na.rm=TRUE)

+    resmid <- resmid[1]+(resmid[2]-resmid[1])/2

+  }

+  if(is.na(resmid)) resmid <- Inf

   function(j, i, x, y, width, height, fill){

     if(value_format=="" || is.null(value_format) || is.na(value_format))

       return(NULL)

@@ -315,7 +324,7 @@ colCenterScale <- function(x, centerFn=median,

     } 

     lab <- gsub("^1.00$","1",lab)

     lab <- gsub("^.00$","0",lab)

-    cols <- ifelse(res2[i,j]>resmid,cols[1],cols[2])

+    cols <- ifelse(res2[i,j]>=resmid,cols[1],cols[2])

     grid.text(lab, x, y, gp = gpar(fontsize = 10*font_factor, col=cols))

   }

 }

@@ -65,10 +65,11 @@ names themselves can also be passed to specify an order, or a

 \item{show_column_names}{Passed to `Heatmap` (default FALSE)}

-\item{col}{Colors for the heatmap. By default, will apply linear mapping (if

+\item{col}{Colors for the heatmap, or a color-mapping function as produced by

+`colorRamp2`. If passing a vector of colors and the data is scaled, there 

+should be an odd number of colors. By default, will apply linear mapping (if

 the data is not scaled) or signed sqrt mapping (if scaled) on the 

-`viridisLite::inferno` palette. To disable the signed sqrt-transformation,

-simply pass `col=viridisLite::inferno(100)` or your own palette.}

+`viridisLite::inferno` palette.}

 \item{font_factor}{A scaling factor applied to fontsizes (default 1)}