Random arc position to avoid overlapping - #11

guigolab · Mar 19, 2021 · f33d4c5 · f33d4c5
1 parent 890cf40
commit f33d4c5
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Showing 4 changed files with 7 additions and 6 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
 ../sashimi-plot.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
-../sashimi-plot.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
+## 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
+../sashimi-plot.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
 
 
diff --git a/examples/sashimi.pdf b/examples/sashimi.pdf
diff --git a/examples/sashimi.tiff b/examples/sashimi.tiff
diff --git a/sashimi-plot.py b/sashimi-plot.py
@@ -802,7 +802,8 @@ def get_debug_info():
                                                 j[4] = ifelse(length(d[x==j[2]+1,y])==0, 0, max(as.numeric(d[x==j[2]+1,y])))
                                         }
                                         if (i%%%%2 != 0) { #top
-                                          maxheight_j = max(maxheight_j, max(j[3:4]) * 1.2)
+                                                set.seed(mean(j[3:4]))
+                                                maxheight_j = max(maxheight_j, max(j[3:4]) * runif(1, 1.2, 1.5))
                                         }
                                 }
                         }
@@ -918,8 +919,8 @@ def get_debug_info():
 
                                 # Find intron midpoint
                                 xmid = round(mean(j[1:2]), 1)
-                                ypad = 0.2*(j[2]-j[1])/(max(d[,x])-min(d[,x]))
-                                ymid = max(j[3:4]) * (1 + ypad)
+                                set.seed(mean(j[3:4]))
+                                ymid = max(j[3:4]) * runif(1, 1.2, 1.5)
 
                                 # Thickness of the arch
                                 lwd = scale_lwd(j[5]/j_tot_counts)
@@ -931,7 +932,7 @@ def get_debug_info():
                                 # Choose position of the arch (top or bottom)
                                 nss = i
                                 if (nss%%%%2 == 0) {  #bottom
-                                        ymid = -(0.2 + ypad) * maxheight
+                                        ymid = -runif(1, 0.2, 0.4) * maxheight
                                         # Draw the arcs
                                         # Left
                                         curve = xsplineGrob(x=c(0, 0, 1, 1), y=c(1, 0, 0, 0), shape=1, gp=curve_par)