cleanup

Figures_manuscript/scripts/Fig_SUP1_genetic__correlation.R

@@ -3,16 +3,16 @@ library(ggplot2)
 library(cowplot)
 library("stringr")
 
-trait_72 = fread("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\inputs\\72trait_data_2023-06-08_sorted.csv")
+trait_72 = fread("../inputs/72trait_data_2023-06-08_sorted.csv")
 head(trait_72)
 trait_72 = trait_72[!is.na(trait_72[,`log10_mes_semilogadjust`]),]
 head(trait_72)
 setkey(trait_72, "ID")
 
-Rho = fread("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\inputs\\Correlation_matrix_genetic.csv")
+Rho = fread("../inputs/Correlation_matrix_genetic.csv")
 setkey(Rho, "V1")
 
-Pval = fread("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\inputs\\Pval_cor_matrix_genetic.csv")
+Pval = fread("../inputs/Pval_cor_matrix_genetic.csv")
 setkey(Pval, "V1")
 
 Rho = Rho[trait_72$ID , c("V1",trait_72$ID), with=FALSE]
@@ -24,9 +24,9 @@ gen_dist[is.na(gen_dist)] = 1
 h = hclust(gen_dist, method="ward.D2")
 clust = cutree(h, h=2)
 
-pdf("V:\\5._ARTICLE_DISCOVERABILITY\\dendro_genet_dist.pdf", width=12)
-  plot(h)
-dev.off()
+#pdf("V:\\5._ARTICLE_DISCOVERABILITY\\dendro_genet_dist.pdf", width=12)
+#  plot(h)
+#dev.off()
 
 for(cl in unique(clust)){
   print(cl)
@@ -76,7 +76,7 @@ pG = pG +  theme(legend.key.size = unit(1, 'cm'), #change legend key size
 pG = pG + geom_text(data=pval_long, aes(x=V1,y=variable, label=pval_annote), size=3.5)
 
 
-png("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\outputs\\Fig_sup_genetic_correlation.png",width = 20, height    = 20,
+png("../outputs/Fig_sup_genetic_correlation.png",width = 20, height    = 20,
   units     = "in",
   res       = 300,
   pointsize = 4)

Figures_manuscript/scripts/Fig_SUP7_gain_vs_numberofjointhits.R

@@ -10,7 +10,7 @@ CV_fold = list()
 
 #for( i in 2:6){
   i=1
-CV_fold[[paste(i,"_train")]] = fread("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\inputs\\JASS_5CVdata-2023-08-01\\traitset_jass_5CVcombined_without_duplicates.tsv")
+CV_fold[[paste(i,"_train")]] = fread("../inputs/JASS_5CVdata-2023-08-01/traitset_jass_5CVcombined_without_duplicates.tsv")
 
       
 #}
@@ -41,7 +41,7 @@ p_joint_hit = p_joint_hit + theme(legend.position = 'top', legend.text = element
 p_joint_hit = p_joint_hit + labs(fill="Test type")
 set_null_device("cairo")
 
-JASS_wth_missing = fread("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\inputs\\JASS_5CVdata-2023-08-01\\stat_set_with_fullJASS_power_5CVcombined_without_duplicates.tsv")
+JASS_wth_missing = fread("../inputs/JASS_5CVdata-2023-08-01/stat_set_with_fullJASS_power_5CVcombined_without_duplicates.tsv")
 head(JASS_wth_missing)
 
 p_joint_hit_wth_missing =  ggplot(JASS_wth_missing, aes(x=Joint)) + geom_histogram(position="dodge", fill="#4287f5", binwidth=1)
@@ -50,7 +50,7 @@ p_joint_hit_wth_missing = p_joint_hit_wth_missing + theme(legend.position = 'top
 p_joint_hit_wth_missing = p_joint_hit_wth_missing + labs(fill="Test type")
 
 
-png("V:\\5._ARTICLE_DISCOVERABILITY\\Figures\\outputs\\Fig_SUP_gain_vs_numberofjointhits.png", width = 8, height = 8,
+png("../outputs/Fig_SUP_gain_vs_numberofjointhits.png", width = 8, height = 8,
   units     = "in",
   res       = 300,
   pointsize = 4)