lineage dist plots combined generated

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scripts/plotting/lineage_dist_PS.R

@@ -1,8 +1,4 @@
 #!/usr/bin/env Rscript  
-getwd()
-setwd("~/git/LSHTM_analysis/scripts/plotting/")
-getwd()
-
 #########################################################
 # TASK: Lineage dist plots: ggridges
 
@@ -14,7 +10,12 @@ getwd()
 ##########################################################
 # 				Installing and loading required packages 			 
 ##########################################################
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting/")
+getwd()
 
+source("Header_TT.R")
+library(ggridges)
 source("combining_dfs_plotting.R")
 # PS combined: 
 # 1) merged_df2
@@ -273,9 +274,9 @@ p2 = ggplot(df_dr, aes(x = duet_scaled
         , axis.ticks.y = element_blank()
         , plot.title = element_blank()
         , strip.text = element_text(size = my_als)
-        #, legend.text = element_text(size = 10)
-        #, legend.title = element_text(size = my_als)
-        , legend.position = "none"
+        , legend.text = element_text(size = 10)
+        , legend.title = element_text(size = my_als)
+        #, legend.position = "none"
   ) 
 
 print(p2)
@@ -288,7 +289,7 @@ print(p2)
 lineage_dist_combined = "lineage_dist_combined_PS.svg"
 plot_lineage_dist_combined  =  paste0(plotdir,"/", lineage_dist_combined)
 
-svg(plot_lineage_dist_combined, width = 16, height = 12)
+svg(plot_lineage_dist_combined, width = 12, height = 6)
 
 printFile = cowplot::plot_grid(p1, p2
                                , label_size = my_als+10)

scripts/plotting/running_plot_scripts

@@ -3,6 +3,9 @@
 #========
 FIXME:
 
+#=======================
+dirs.R
+#=======================
 #dirs.R: imports dir structure
 change this to cmd so you can pass in drug and gene name
 
@@ -11,6 +14,13 @@ plotting_data.R
 #=======================
 ??? update how to run
 
+
+#=======================
+combining_dfs_plotting.R
+#=======================
+??? update how to run
+
+
 #=======================
 mcsm_mean_stability.R
 #=======================
@@ -62,6 +72,13 @@ barplots_subcolours_PS.R
 # output plots: 1 svg
     1) barplot_coloured_PS.svg
 
+#=======================
+lineage_dist_PS.R
+# lineage distribution for all muts and dr muts in one figure
+#=======================
+# input: calls the "combining_dfs_plotting.R"
+# output plots: 1 svg
+    1) lineage_dist_combined_PS.svg
 
     
 ########################################################################