Fix median aggregation - close #69

guigolab · Oct 18, 2021 · 143dbd9 · 143dbd9
1 parent 39c5826
commit 143dbd9
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/examples/example_run.sh b/examples/example_run.sh
@@ -5,7 +5,7 @@
 ## Example #1. Overlay, intron shrinkage, gene annotation, PDF output, custom size and colors
 ../ggsashimi.py -b input_bams.tsv -c chr10:27040584-27048100 -g annotation.gtf -M 10 -C 3 -O 3 --shrink --alpha 0.25 --base-size=20 --ann-height=4 --height=3 --width=18 -P palette.txt
 
-## Example #2. Median coverage and number of reads supporting inclusion and exclusion, no gene annotation, TIFF output (350 PPI), custom size, default colors, fixed y-scale
-../ggsashimi.py -b input_bams.tsv -c chr10:27040584-27048100 -M 10 -C 3 -O 3 -A median --alpha 1 -F tiff -R 350 --base-size=16 --height=3 --width=18 --fix-y-scale
+## Example #2. Mean coverage and number of reads supporting inclusion and exclusion, no gene annotation, TIFF output (350 PPI), custom size, default colors, fixed y-scale
+../ggsashimi.py -b input_bams.tsv -c chr10:27040584-27048100 -M 10 -C 3 -O 3 -A mean --alpha 1 -F tiff -R 350 --base-size=16 --height=3 --width=18 --fix-y-scale
 
 
diff --git a/ggsashimi.py b/ggsashimi.py
@@ -794,7 +794,7 @@ def get_debug_info():
                                 row_i = c()
                                 if (nrow(junctions) >0 ) {
                                         junctions$jlabel = as.character(junctions$count)
-                                        junctions = setNames(junctions[,.(max(y), max(yend),round(mean(count)),paste(jlabel,collapse=",")), keyby=.(x,xend)], names(junctions))
+                                        junctions = setNames(junctions[,.(max(y), max(yend),round(%(args.aggr)s(count)),paste(jlabel,collapse=",")), keyby=.(x,xend)], names(junctions))
                                         if ("%(args.aggr)s" != "") {
                                                 junctions = setNames(junctions[,.(max(y), max(yend),round(%(args.aggr)s(count)),round(%(args.aggr)s(count))), keyby=.(x,xend)], names(junctions))
                                         }
@@ -902,7 +902,7 @@ def get_debug_info():
                         if (nrow(junctions) >0 ) {
 
                                 junctions$jlabel = as.character(junctions$count)
-                                junctions = setNames(junctions[,.(max(y), max(yend),round(mean(count)),paste(jlabel,collapse=",")), keyby=.(x,xend)], names(junctions))
+                                junctions = setNames(junctions[,.(max(y), max(yend),round(%(args.aggr)s(count)),paste(jlabel,collapse=",")), keyby=.(x,xend)], names(junctions))
                                 if ("%(args.aggr)s" != "") {
                                         junctions = setNames(junctions[,.(max(y), max(yend),round(%(args.aggr)s(count)),round(%(args.aggr)s(count))), keyby=.(x,xend)], names(junctions))
                                 }