dadded v2 of barplot layput

2022-08-14 22:56:08 +01:00 · 2022-08-14 22:56:08 +01:00 · 7c40e13771
commit 7c40e13771
parent da8f8d90d4
7 changed files with 800 additions and 79 deletions
--- a/scripts/plotting/plotting_thesis/bp_PE.R
+++ b/scripts/plotting/plotting_thesis/bp_PE.R
@ -0,0 +1,182 @@
+colnames(str_df_short)
+table(str_df_short$effect_type)
+table(str_df_short$effect_sign)
+
+str(str_df_short)
+
+str_df_short$pe_outcome = ifelse(str_df_short$effect_sign<0, "DD", "SS")
+table(str_df_short$pe_outcome )
+table(str_df_short$effect_sign)
+
+affcols = c("affinity_scaled",  "mmcsm_lig_scaled")
+ppi2_cols = c("mcsm_ppi2_scaled")
+
+#lig 
+table(str_df_short$effect_type)
+
+str_df_short$effect_grouped = ifelse(str_df_short$effect_type%in%affcols
+                                     , "affinity"
+                                     , str_df_short$effect_type)
+table(str_df_short$effect_grouped)
+
+#ppi2
+str_df_short$effect_grouped = ifelse(str_df_short$effect_grouped%in%ppi2_cols
+                                     , "ppi2"
+                                     , str_df_short$effect_grouped)
+table(str_df_short$effect_grouped)
+
+#stability
+str_df_short$effect_grouped = ifelse(!str_df_short$effect_grouped%in%c("affinity", "ppi2")
+                                     , "stability"
+                                     , str_df_short$effect_grouped)
+
+table(str_df_short$effect_grouped)
+
+
+# create a sign as well
+str_df_short$effect_outcome = paste0(str_df_short$pe_outcome
+                                     , str_df_short$effect_grouped)
+
+table(str_df_short$effect_outcome)
+
+pe_colour_map2 = c(   "DDaffinity"    = 	"#ffd700" # gold
+                  ,    "SSaffinity"    = 	"#f0e68c" # khaki
+                  ,  "DDppi2"        =  "#ff1493" # deeppink
+                  ,  "SSppi2"         =  "#da70d6" # orchid
+                  ,  "DDstability "  =  "#ae301e"
+                  ,  "SSstability"    =  "#007d85"
+)
+
+
+str_df_short$effect_colours = str_df_short$effect_outcome
+
+str_df_short = dplyr::mutate(str_df_short
+                         , effect_colours = case_when(effect_colours == "DDaffinity" ~ "#ffd700"
+                                                  , effect_colours == "DDppi2" ~ '#ff1493'
+                                                  , effect_colours == "SSppi2" ~ '#da70d6' 
+                                                  , effect_colours == "DDstability" ~ '#ae301e'
+                                                  , effect_colours =="SSstability" ~ '#007d85'
+                                                  , TRUE ~ 'ns'))
+
+"#F8766D" #red
+"#00BFC4" #blue
+table(str_df_short$effect_colours)
+
+
+###########################################
+
+ggplot(str_df_short
+       , aes( x=effect_grouped
+              , fill = effect_colours)) + 
+  geom_bar() +
+    scale_fill_manual(values = str_df_short$effect_colours)
+
+
+
+first_col  = c(38, 0)
+second_col = c(9, 22)
+third_col  = c(681, 108)
+thing_df = data.frame(first_row, second_row, third_row)
+rownames(thing_df) = c("Destabilising","Stabilising")
+thing_df
+
+
+###############################################
+rect_colour_map = c("EMB"   = "green"
+                    ,"DSL"  = "slategrey"
+                    , "CDL" = "navyblue"
+                    , "Ca"  = "purple")
+
+
+rects <- data.frame(x = 1:6,
+                    colors = c("#ffd700" #gold
+                               , "#f0e68c" #khaki
+                               , "#da70d6"# orchid
+                               , "#ff1493"# deeppink
+                               , "#00BFC4" #, "#007d85" #blue
+                               , "#F8766D" )# red,
+)
+rects
+
+rects$text =  c("-ve Lig affinty"
+                , "+ve Lig affinity"
+                , "+ve PPI2 affinity"
+                , "-ve PPI2 affinity"
+                , "+ve stability"
+                , "-ve stability")
+
+
+rects$numbers = c(38, 0, 22, 9, 108, 681)
+rects$num_labels = paste0("n=", rects$numbers)
+
+rects
+
+outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
+
+#https://stackoverflow.com/questions/47986055/create-a-rectangle-filled-with-text
+png(paste0(outdir_images, "test.png")
+    , width = 0.5
+    , height = 2.5
+    , units = "in", res = 300)
+
+ggplot(rects, aes(x, y = 0, fill = colors, label = paste0(text,"\n", num_labels))) +
+  geom_tile(width = 1, height = 1) + # make square tiles
+  geom_text(color = "black", size = 1.5) + # add white text in the middle
+  scale_fill_identity(guide = "none") + # color the tiles with the colors in the data frame
+  coord_fixed() + # make sure tiles are square
+  coord_flip()+ scale_x_reverse() +
+ # theme_void() # remove any axis markings
+  theme_nothing() # remove any axis markings
+  
+
+dev.off()
+
+
+
+
+
+
+
+##########################################################
+tile_map=data.frame(tile=c("EMB","DSL","CDL","Ca")
+                    ,tile_colour =c("green","darkslategrey","navyblue","purple"))
+
+
+# great
+tile_colour_map = c("EMB"   = "green"
+                    ,"DSL"  = "darkslategrey"
+                    , "CDL" = "navyblue"
+                    , "Ca"  = "purple")
+
+tile_legend=get_legend(
+  
+  ggplot(tile_map, aes(factor(tile),y=0
+                       , colour=tile_colour
+                       , fill=tile_colour))+
+    geom_tile() +
+    theme(legend.direction="horizontal") +
+    scale_colour_manual(name=NULL
+                        #, values = tile_map$tile_colour
+                        , values=tile_colour_map) +
+    scale_fill_manual(name=NULL 
+                      #,values=tile_map$tile_colour
+                      , values = tile_colour_map)
+)
+#############################################################
+
+
+###############################################
+library(ggplot2)
+library(viridis)
+library(hrbrthemes)
+
+ggplot(str_df_short, aes(fill=effect_colours,x=effect_type)) + 
+  geom_bar() +
+  
+  scale_fill_viridis(discrete = T) +
+  ggtitle("Studying 4 species..") 
+####################################################
+
+
+
+