Merge pull request #114 from uclahs-cds/Phils-replot_box

Update plot_num_subclones_box.R
uclahs-cds · Jan 22, 2024 · 016c4a6 · 016c4a6
2 parents 1b3da15 + 5373f5e
commit 016c4a6
Showing 1 changed file with 38 additions and 38 deletions.
diff --git a/src/output-analysis/plotting/plot_num_subclones_box.R b/src/output-analysis/plotting/plot_num_subclones_box.R
@@ -26,38 +26,41 @@ subclones.data <- read.table(file = args$file, sep = '\t', header = TRUE);
 src.tool <- strsplit(args$pipeline, '-')[[1]][3];
 src.colour <- pipeline.colour.scheme[src.tool];
 
+filename <- paste0('2024_01_01-', args$pipeline, '_', args$mode, '_subclones_box.pdf');
+print(filename);
+
 ### SR FUNCTION ###################################################################################
 plot.sr <- function(df) {
     plot <- create.boxplot(
-        formula = n_clones ~ patient,
-        data = subclones.data,
+        formula = patient ~ n_clones,
+        data = df,
         filename = generate.filename(
             'proj-seed',
             paste0(args$pipeline, '_', args$mode, '_subclones_box'),
             'pdf'
             ),
         main = args$pipeline,
-        ylab.label = 'Number of Subclones',
-        xlab.label = 'Patient',
+        xlab.label = 'Number of Subclones',
+        ylab.label = 'Patient',
         main.just = 'center',
         main.x = 0.52,
-        ylimits = c(0.5, 9.5),
-        yat = seq(1, 9, 1),
-        xaxis.lab = patients.sr,
+        xlimits = c(0.5, 9.5),
+        xat = seq(1, 9, 1),
+        yaxis.lab = patients.sr,
         add.stripplot = TRUE,
         points.pch = 19,
         points.col = 'black',
         points.cex = 0.4,
         points.alpha = 1,
         col = src.colour,
         alpha.rectangle = 0.8,
-        main.cex = 1.1,
-        xaxis.cex = 0.8,
-        yaxis.cex = 0.8,
-        xlab.cex = 1.1,
-        ylab.cex = 1.1,
+        main.cex = 1.6,
+        xaxis.cex = 1.6,
+        yaxis.cex = 1.6,
+        xlab.cex = 1.6,
+        ylab.cex = 1.6,
         xaxis.tck = c(1, 0),
-        yaxis.tck = c(1, 0),
+        yaxis.tck = c(1, 0, 1),
         xaxis.rot = 0,
         xaxis.fontface = 1,
         yaxis.fontface = 1,
@@ -67,57 +70,54 @@ plot.sr <- function(df) {
         left.padding = 1,
         ylab.axis.padding = 1,
         description = 'Boxplot created by BoutrosLab.plotting.general',
-        height = 4,
-        width = 7
+        height = 8,
+        width = 4
         );
     };
 
 ### MR FUNCTION ###################################################################################
 plot.mr <- function(df) {
     plot <- create.boxplot(
-        formula = n_clones ~ patient,
-        data = subclones.data,
+        formula = patient ~ n_clones,
+        data = df,
         filename = generate.filename(
             'proj-seed',
             paste0(args$pipeline, '_', args$mode, '_subclones_box'),
             'pdf'
             ),
         main = args$pipeline,
-        ylab.label = 'Number of Subclones',
-        xlab.label = 'Patient',
+        xlab.label = 'Number of Subclones',
+        ylab.label = 'Patient',
         main.just = 'center',
         main.x = 0.52,
-        ylimits = c(0.5, 9.5),
+        xlimits = c(0.5, 9.5),
+        xat = seq(1, 9, 1),
+        yaxis.lab = patients.mr,
         yat = seq(1, 9, 1),
-        xaxis.lab = patients.mr,
         add.stripplot = TRUE,
         points.pch = 19,
         points.col = 'black',
-        points.cex = 0.6,
+        points.cex = 0.4,
         points.alpha = 1,
         col = src.colour,
         alpha.rectangle = 0.8,
-        main.cex = 1.1,
-        xaxis.cex = 0.8,
-        yaxis.cex = 0.8,
-        xlab.cex = 1.1,
-        ylab.cex = 1.1,
+        main.cex = 1.6,
+        xaxis.cex = 1.6,
+        yaxis.cex = 1.6,
+        xlab.cex = 1.6,
+        ylab.cex = 1.6,
         xaxis.tck = c(1, 0),
         yaxis.tck = c(1, 0),
         xaxis.rot = 0,
         xaxis.fontface = 1,
         yaxis.fontface = 1,
-        top.padding = 1,
+        top.padding = 35,
         bottom.padding = 1,
         right.padding = 1,
         left.padding = 1,
         ylab.axis.padding = 1,
-        description = 'Boxplot created by BoutrosLab.plotting.general',
-        #legend = list(
-        #    right = list(fun = algorithm.legends.grob)
-        #    ),
-        height = 4,
-        width = 7
+        size.units = 'inches',
+        description = 'Boxplot created by BoutrosLab.plotting.general'
         );
     };
 
@@ -127,7 +127,7 @@ setwd(args$output);
 if (args$mode == 'sr') {
     plot.sr(subclones.data)
     print('plotting sr')
-  } else {
-      plot.mr(subclones.data)
-      print('plotting mr')
-      };
+} else {
+    plot.mr(subclones.data)
+    print('plotting mr')
+    };