add consurf-only scripts

scripts/plotting/plotting_thesis/katg/consurf-plot.R

@@ -0,0 +1,54 @@
+# katg ONLY
+source("~/git/LSHTM_analysis/config/katg.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/katg/"
+
+w=4.5
+h=4.5
+
+consurfP = stability_count_bp(plotdf = df3
+                              , df_colname = "consurf_outcome"
+                              , yaxis_title = "Number of SAVs"
+                              , leg_position = "none"
+                              #, subtitle_text = "ConSurf"
+                              , bar_fill_values = consurf_colours
+                              , subtitle_colour= "black"
+                              , sts = sts
+                              , lts = lts
+                              , ats = ats
+                              , als = als
+                              , ltis = ltis
+                              , geom_ls = geom_ls)
+
+consurf_legend = get_legend(
+  ggplot(df3, aes(factor(consurf_outcome))) +
+    geom_tile(aes(
+      fill = consurf_outcome, y=0
+    )
+    )+
+    
+    scale_fill_manual(
+      values=consurf_colours,
+      labels=c("0\nND","1\nVar","2","3","4","5\nAvg","6","7","8","9\nCons"),
+      guide=guide_legend(title="Consurf",
+                         title.position = "top",
+                         title.hjust = 0.5,
+                         label.position = "bottom",
+                         nrow = 1
+      )
+    )
+)
+
+consurf_out=cowplot::plot_grid(consurf_legend, consurfP,ncol=1,rel_heights = c(2.5,12))
+
+conCLP =  paste0(outdir_images
+                 ,tolower(gene)
+                 ,"_consurf_BP.jpg")
+
+print(paste0("plot filename:", conCLP))
+jpeg(conCLP, units = "in", width = w, height = h, res = 300 )
+consurf_out
+
+dev.off()