diff --git a/Figures_manuscript/scripts/Fig_SUP1_genetic__correlation.R b/Figures_manuscript/scripts/Fig_SUP1_genetic__correlation.R index d499f277275190e13ee4a69e316a891c5bd3e649..2982b0d09a6a929289da67cd1455b196ed1363c9 100644 --- a/Figures_manuscript/scripts/Fig_SUP1_genetic__correlation.R +++ b/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) diff --git a/Figures_manuscript/scripts/Fig_SUP7_gain_vs_numberofjointhits.R b/Figures_manuscript/scripts/Fig_SUP7_gain_vs_numberofjointhits.R index d0284c58f312af105f94ec03454ba5a2630806c5..3e6a41b103d55c6e17c54c439858eba0c9f37243 100644 --- a/Figures_manuscript/scripts/Fig_SUP7_gain_vs_numberofjointhits.R +++ b/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)