added dir for embb for consistency and checks and moved others to version1

scripts/plotting/plotting_thesis/gg_pairs.R

@@ -1,56 +0,0 @@
-# Tweak for layout, fonts, and text sizes.
-#svg('~/tmp/foo.svg', width=10, height=10, )
-
-
-# Set the width/height to inches for print. 300 dpi is reasonably ok for "draft"
-# output. To raise quality while preserving sanity, increase 'res' and
-# DO NOT alter font/point/line sizes
-
-
-
-#- [X] Black text for "Corr:" or replace with Rho symbol
-#- [X] 0/1 == R/S
-#- [X] "rho" symbol instead of "Corr:" text
-#- [X] Dot size a bit smaller
-#- [X] Plot lines slightly thinner
-# 
-# 
-png('~/tmp/foo.png',
-    width=10,
-    height=10,
-    units="in",
-    res=300)
-# 
-#corr_plotting_df = corr_df_ps
-colnames(corr_plotdf)
-corr_plotting_df = subset(corr_plotdf, select = -c(ethambutol,`Log10(OR)`,`-Log10(P)`, ASA, RSA, KD, RD
-                                                   , FoldX
-                                                   , DeepDDG
-                                                   , Dynamut2 ))
-colnames(corr_plotting_df)
-#ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)-1),
-ggpairs(corr_plotting_df, columns = 1:(ncol(corr_plotting_df)),
-                
-        upper = list(continuous = wrap('cor',
-                                       method = "spearman",
-                                       use = "pairwise.complete.obs",
-                                       title="ρ",
-                                       digits=2,
-                                       title_args=c(colour="black")
-                                       )
-                     ),
-        lower = list(
-          continuous = wrap("points", alpha = 0.7, size=0.5),
-          combo     = wrap("dot", alpha = 0.7, size=0.5)
-        ),
-        aes(colour = factor(ifelse(dst_mode==0, "S", "R")), alpha = 0.5),
-        title="Stability") +
-  
-  scale_colour_manual(values = c("red", "blue")) +
-  scale_fill_manual(values = c("red", "blue")) + 
-  theme(
-    text = element_text(size=12, face="bold")
-  )
-
-dev.off()
-#Check all plots with LSHTM_analysis/scripts/plotting/plotting_colnames.R