add consurf-only scripts

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

@@ -0,0 +1,54 @@
+# alr ONLY
+source("~/git/LSHTM_analysis/config/alr.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/alr/"
+
+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()

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

@@ -0,0 +1,54 @@
+# embb ONLY
+source("~/git/LSHTM_analysis/config/embb.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/embb/"
+
+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()

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

@@ -0,0 +1,54 @@
+# gid ONLY
+source("~/git/LSHTM_analysis/config/gid.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/gid/"
+
+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()

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()

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

@@ -0,0 +1,54 @@
+# pnca ONLY
+source("~/git/LSHTM_analysis/config/pnca.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/pnca/"
+
+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()

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

@@ -0,0 +1,54 @@
+# rpob ONLY
+source("~/git/LSHTM_analysis/config/rpob.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R")
+
+outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/rpob/"
+
+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()

scripts/plotting/plotting_thesis/thesis-figs-alr.R

@@ -81,9 +81,9 @@ tile_legend=get_legend(
       legend.direction="horizontal",
       legend.text = element_text(size=10),
       legend.key.size = unit(10, "pt")) +
-    scale_colour_manual(name="Active Site"
+    scale_colour_manual(name="Active Site:"
                         , values=tile_colour_map) +
-    scale_fill_manual(name="Active Site" 
+    scale_fill_manual(name="Active Site:" 
                       , values = tile_colour_map)
 )
 
@@ -231,7 +231,7 @@ logo_or_centre = LogoPlotCustomH(
   lig3_colour = tile_map$tile_colour[4]
 )
 
-stability_centre = stab()
+stability_centre = stab(my_ylab="SAV Count")
 
 # HIGH
 small_df3 = merged_df3[merged_df3['position'] > centre,]

scripts/plotting/plotting_thesis/thesis-figs-embb.R

@@ -7,8 +7,8 @@
 # mutable_df3  = cbind(small_df3)
 # plot_df = cbind(small_df3)
 
-#source("~/git/LSHTM_analysis/config/embb.R")
+source("~/git/LSHTM_analysis/config/embb.R")
-#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
 #outdir="/home/pub/Work/LSHTM/Thesis_Plots/"
 outdir="~/git/Writing/thesis/tex/images-corrected/embb/"
@@ -122,9 +122,9 @@ tile_legend=get_legend(
       legend.direction="horizontal",
       legend.text = element_text(size=10),
       legend.key.size = unit(10, "pt")) +
-    scale_colour_manual(name="Active Site"
+    scale_colour_manual(name="Active Site:"
                         , values=tile_colour_map) +
-    scale_fill_manual(name="Active Site" 
+    scale_fill_manual(name="Active Site:" 
                       , values = tile_colour_map)
 )
 

scripts/plotting/plotting_thesis/thesis-figs-gid.R

@@ -78,9 +78,9 @@ tile_legend=get_legend(
       legend.direction="horizontal",
       legend.text = element_text(size=10),
       legend.key.size = unit(10, "pt")) +
-    scale_colour_manual(name="Active Site"
+    scale_colour_manual(name="Active Site:"
                         , values=tile_colour_map) +
-    scale_fill_manual(name="Active Site" 
+    scale_fill_manual(name="Active Site:" 
                       , values = tile_colour_map)
 )
 
@@ -249,7 +249,7 @@ logo_p_snps_high = LogoPlotSnps(
                                 lig1_colour = tile_map$tile_colour[2],
                                 lig2_colour = tile_map$tile_colour[3],
                                 lig3_colour = tile_map$tile_colour[4]
-)
+)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
 
 logo_or_high = LogoPlotCustomH(
                                small_df3, 
@@ -265,7 +265,7 @@ logo_or_high = LogoPlotCustomH(
                                lig1_colour = tile_map$tile_colour[2],
                                lig2_colour = tile_map$tile_colour[3],
                                lig3_colour = tile_map$tile_colour[4]
-)
+)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)
 
 
 stability_high   = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3)

scripts/plotting/plotting_thesis/thesis-figs-katg.R

@@ -80,9 +80,9 @@ tile_legend=get_legend(
       legend.direction="horizontal",
       legend.text = element_text(size=10),
       legend.key.size = unit(10, "pt")) +
-    scale_colour_manual(name="Active Site"
+    scale_colour_manual(name="Active Site:"
                         , values=tile_colour_map) +
-    scale_fill_manual(name="Active Site" 
+    scale_fill_manual(name="Active Site:" 
                       , values = tile_colour_map)
 )
 

scripts/plotting/plotting_thesis/thesis-figs-rpob.R

@@ -79,9 +79,9 @@ tile_legend=get_legend(
       legend.direction="horizontal",
       legend.text = element_text(size=10),
       legend.key.size = unit(10, "pt")) +
-    scale_colour_manual(name="Active Site"
+    scale_colour_manual(name="Active Site:"
                         , values=tile_colour_map) +
-    scale_fill_manual(name="Active Site" 
+    scale_fill_manual(name="Active Site:" 
                       , values = tile_colour_map)
 )