diff --git a/scripts/plotting/ggcorr_all_PS_LIG.R b/scripts/plotting/ggcorr_all_PS_LIG.R index aa35922..d6fe43b 100644 --- a/scripts/plotting/ggcorr_all_PS_LIG.R +++ b/scripts/plotting/ggcorr_all_PS_LIG.R @@ -10,13 +10,14 @@ getwd() setwd("~/git/LSHTM_analysis/scripts/plotting/") getwd() - source("Header_TT.R") require(cowplot) source("combining_dfs_plotting.R") -source("my_pairs_panel.R") +#source("my_pairs_panel.R") # should return the following dfs, directories and variables +# FIXME: Can't output from here + # PS combined: # 1) merged_df2 # 2) merged_df2_comp @@ -56,15 +57,17 @@ cat(paste0("Variables imported:" #plot_corr_plot_combined = paste0(plotdir,"/", corr_plot_combined) # PS -ggcorr_all_ps = "ggcorr_all_PS.svg" +#ggcorr_all_ps = "ggcorr_all_PS.svg" +ggcorr_all_ps = "ggcorr_all_PS.png" plot_ggcorr_all_ps = paste0(plotdir,"/", ggcorr_all_ps) # LIG -ggcorr_all_lig = "ggcorr_all_LIG.svg" +#ggcorr_all_lig = "ggcorr_all_LIG.svg" +ggcorr_all_lig = "ggcorr_all_LIG.png" plot_ggcorr_all_lig = paste0(plotdir,"/", ggcorr_all_lig ) # combined -ggcorr_all_combined_labelled = "ggcorr_all_combined_labelled.svg" +ggcorr_all_combined_labelled = "ggcorr_all_combined_labelled.png" plot_ggcorr_all_combined_labelled = paste0(plotdir,"/", ggcorr_all_combined_labelled) #################################################################### @@ -237,15 +240,14 @@ pmat1==pmat2 # Generate ggcorr PS plot #------------------------ cat("ggCorr plot PS:", plot_ggcorr_all_ps) -svg(plot_ggcorr_all_ps, width = 15, height = 15) - +#png(filename = plot_ggcorr_all_ps, width = 1024, height = 768, units = "px", pointsize = 20) ggcorr_ps = ggcorrplot(corr1 , p.mat = pmat1 , hc.order = TRUE , outline.col = "black" , ggtheme = ggplot2::theme_gray , colors = c("#6D9EC1", "white", "#E46726") - , title = "Spearman correlations with DUET and Foldx stability") + , title = "DUET and Foldx stability") ggcorr_ps @@ -356,7 +358,8 @@ pmat1_lig == pmat2_lig # Generate ggcorr LIG plot #------------------------ cat("ggCorr LIG plot:", plot_ggcorr_all_lig) -svg(plot_ggcorr_all_lig, width = 15, height = 15) +#svg(plot_ggcorr_all_lig, width = 15, height = 15) +#png(plot_ggcorr_all_lig, width = 1024, height = 768, units = "px", pointsize = 20) ggcorr_lig = ggcorrplot(corr1_lig , p.mat = pmat1_lig @@ -365,7 +368,7 @@ ggcorr_lig = ggcorrplot(corr1_lig , ggtheme = ggplot2::theme_gray , colors = c("#6D9EC1", "white", "#E46726") - , title = "Spearman correlations with ligand affinty") + , title = "Ligand affinty") ggcorr_lig @@ -375,15 +378,4 @@ ggcorr_lig #============================= # combine plots for output #============================= -cat("Output plot:", plot_ggcorr_all_combined_labelled) -svg(plot_ggcorr_all_combined_labelled , width = 30, height = 10) - -ggcorr_combined = cowplot::plot_grid(ggcorr_ps, ggcorr_lig - , nrow = 1 - , align = "h" - , labels = c("(a)","(b)") - #, rel_heights = c(1, 1) - #, rel_widths = c(0.85, 1, 1) - , label_size = 25) - -dev.off() ++ \ No newline at end of file