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

scripts/plotting/plotting_thesis/version1/gg_pairs.R

@@ -0,0 +1,56 @@
+# 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