Quick changes to allow plotting of SV calls - new rule for simulated variants

Snakefile

@@ -168,17 +168,35 @@ rule plot_mosaic_counts:
         {params.plot_command} {input.counts} {input.info} {output} > {log} 2>&1
         """
 
+ruleorder: plot_SV_calls_simulated > plot_SV_calls
+
 rule plot_SV_calls:
     input:
         counts = "counts/{sample}/{windows}.txt.gz",
-        calls  = "sv_calls/{sample}/{windows}.{bpdens}/{method}.txt"
+        calls  = "sv_calls/{sample}/{windows}.{bpdens}/{method}.txt",
+        segments = "segmentation2/{sample}/{windows}.{bpdens}.txt"
     output:
         "sv_calls/{sample}/{windows}.{bpdens}/{method}.{chrom}.pdf"
     shell:
         """
-        Rscript utils/chrom.R calls={input.calls} {input.counts} {wildcards.chrom} {output}
+        Rscript utils/chrom.R segments={input.segments} calls={input.calls} {input.counts} {wildcards.chrom} {output}
         """
 
+rule plot_SV_calls_simulated:
+    input:
+        counts = "counts/simulation{seed}-{window}/{window}_fixed.txt.gz",
+        calls  = "sv_calls/simulation{seed}-{window}/{window}_fixed.{bpdens}/{method}.txt",
+        segments = "segmentation2/simulation{seed}-{window}/{window}_fixed.{bpdens}.txt",
+        truth  = "simulation/variants/genome{seed}-{window}.txt"
+    output:
+        "sv_calls/simulation{seed}-{window}/{window}_fixed.{bpdens}/{method}.{chrom}.pdf"
+    shell:
+        """
+        Rscript utils/chrom.R segments={input.segments} truth={input.truth} calls={input.calls} {input.counts} {wildcards.chrom} {output}
+        """
+
+
+
 
 ################################################################################
 # Read counting                                                                #

utils/chrom.R

@@ -43,6 +43,7 @@ manual_colors = c(
   simul_inv_dup   = "darkgoldenrod2",
   idup_h1         = muted("darkgoldenrod2", 80, 70),
   idup_h2         = muted("darkgoldenrod2", 80, 70),
+  complex         = "grey",
     # background
   bg1 = "#ffffff",
   bg2 = "khaki2")
@@ -157,7 +158,10 @@ if (!is.null(f_calls)) {
               "end"      %in% colnames(svs),
               "sample"   %in% colnames(svs),
               "cell"     %in% colnames(svs),
-              "SV_class" %in% colnames(svs)) %>% invisible
+              ("SV_class" %in% colnames(svs) | "sv_call_name" %in% colnames(svs) )) %>% invisible
+  if(!("SV_class" %in% colnames(svs))) {
+    svs[, SV_class := sv_call_name]
+  }
   assert_that(all(svs$SV_class %in% names(manual_colors))) %>% invisible
   svs[, sample_cell := paste(sample, "-", cell)]
   assert_that(all(unique(svs$sample_cell) %in% unique(counts$sample_cell))) %>% invisible