fixed error in scaled heatmap from GRanges/RleList

ETHZ-INS · May 16, 2024 · 91c3f5a · 91c3f5a
1 parent 3973d62
commit 91c3f5a
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: epiwraps
 Type: Package
 Title: epiwraps: Wrappers for plotting and dealing with epigenomics data
-Version: 0.99.90
-Date: 2024-04-29
+Version: 0.99.91
+Date: 2024-05-16
 Authors@R: c(
     person("Pierre-Luc", "Germain", email="pierre-luc.germain@hest.ethz.ch", 
             role=c("cre","aut"), comment=c(ORCID="0000-0003-3418-4218")),

diff --git a/R/misc.R b/R/misc.R
@@ -273,6 +273,8 @@ head(paste(missingLvls, collapse=", "), 3))
     if(is.list(tracks)) tracks <- tracks[[1]]
     if(is(tracks, "GRanges")){
       sl <- seqlengths(tracks)
+    }else if(is(tracks, "RleList")){
+      sl <- lengths(tracks)
     }else if(.parseFiletypeFromName(tracks)=="bw"){
       sl <- seqlengths(BigWigFile(tracks))
     }else if(.parseFiletypeFromName(tracks)=="bam"){

diff --git a/R/signal2Matrix.R b/R/signal2Matrix.R
@@ -135,7 +135,7 @@ signal2Matrix <- function(filepaths, regions, extend=2000, w=NULL, scaling=TRUE,
     filepath <- filepaths[[filename]]
     if(is(filepath, "GRanges")){
       if(verbose) message("Computing signal from GRanges '", filename, "'...")
-    }else{
+    }else if(!is(filepath, "RleList")){
       if(verbose) message("Reading ", filepath)
       if(grepl("\\.rds$",filepath,ignore.case=TRUE))
         filepath <- readRDS(filepath)
@@ -144,7 +144,7 @@ signal2Matrix <- function(filepaths, regions, extend=2000, w=NULL, scaling=TRUE,
     if(is(filepath, "GRanges")){
 
       ####### GRanges INPUT
-      if(type=="scale"){
+      if(type=="scaled"){
         target_ratio <- w*scaledBins/sum(extend)
         mat <- normalizeToMatrix(filepath, regions, w=w, extend=extend, 
                                  value_column="score", mean_mode="absolute", 
@@ -156,6 +156,8 @@ signal2Matrix <- function(filepaths, regions, extend=2000, w=NULL, scaling=TRUE,
       }
       ####### END GRanges INPUT
 
+    }else if(is(filepath, "RleList")){
+      co <- filepath
     }else if(grepl("\\.bam$",filepath,ignore.case=TRUE)){
 
       ####### BAM INPUT
@@ -188,8 +190,6 @@ signal2Matrix <- function(filepaths, regions, extend=2000, w=NULL, scaling=TRUE,
       co <- rtracklayer::import(filepath, format="BigWig", as="RleList",
                                 selection=BigWigSelection(readRegions))
 
-    }else if(is(filepath, "RleList")){
-      co <- filepath
     }else{
       stop("Unknown file format")
     }