Merge pull request #93 from DIncalciLab/add-plot-name

Allow adding the plot name to the genome plots
CenterForMedicalGeneticsGhent · Sep 7, 2022 · ad25dce · ad25dce
2 parents 98a3678 + be82584
commit ad25dce
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Showing 3 changed files with 19 additions and 2 deletions.
diff --git a/wisecondorX/include/plotter.R b/wisecondorX/include/plotter.R
@@ -7,6 +7,7 @@ options(warn=-1)
 args <- commandArgs(T)
 in.file <- paste0(args[which(args == "--infile")+1])
 
+
 # -----
 # lib
 # -----
@@ -29,6 +30,7 @@ gender = input$ref_gender
 beta = as.numeric(input$beta)
 zcutoff = as.numeric(input$zscore)
 ylim = input$ylim
+plot.title = input$plot_title
 
 if (input$cairo) options(bitmaptype='cairo')
 
@@ -209,6 +211,12 @@ legend(x=0,
        cex=1.3, bty="n", pch=c(16,16), col=c(color.C, color.B, "white"))
 par(xpd=F)
 
+if (!is.null(plot.title)) {
+    par(xpd=NA)
+    title(plot.title, line=1.3, adj=0.8, col.main=color.A)
+    par(xpd=F)
+}
+
 # plot segmentation
 
 for (ab in input$results_c){
@@ -278,7 +286,7 @@ for (c in chrs){
   if (any(is.na(whis))){
     next
   }
-  
+
   png(paste0(out.dir, "/", labels[c],".png"), width=14,height=10,units="in",res=256,pointsize=18)
 
   upper.limit <- 0.6 + whis[2]
@@ -289,7 +297,7 @@ for (c in chrs){
     lower.limit = ylim[1] ; upper.limit = ylim[2]
   }
   par(mar=c(2.5,4,1,0), mgp=c(2.4,0.5,0))
-  
+
   plot(1, main="", axes=F, # plots nothing -- enables segments function
        xlab="", ylab="", cex=0, ylim=c(lower.limit,upper.limit), xlim=margins)
 

diff --git a/wisecondorX/main.py b/wisecondorX/main.py
@@ -396,6 +396,9 @@ def main():
     parser_test.add_argument('--cairo',
                              action='store_true',
                              help='Uses cairo bitmap type for plotting. Might be necessary for certain setups.')
+    parser_test.add_argument("--add-plot-title",
+                             action="store_true",
+                             help="Add the output name as plot title")
     parser_test.set_defaults(func=tool_test)
 
     args = parser.parse_args(sys.argv[1:])

diff --git a/wisecondorX/predict_output.py b/wisecondorX/predict_output.py
@@ -28,6 +28,12 @@ def exec_write_plots(rem_input, results):
         'infile': str('{}.json'.format(json_plot_dir)),
         'out_dir': str('{}.plots'.format(rem_input['args'].outid)),
     }
+
+    if rem_input["args"].add_plot_title:
+        # Strip away paths from the outid if need be
+        json_dict["plot_title"] = str(
+            os.path.basename(rem_input["args"].outid))
+
     exec_R(json_dict)