attempting to visualise consurf plot along with highlighting active site pos

2022-02-02 19:00:23 +00:00 · 2022-02-02 19:00:23 +00:00 · 3e5191f5c6
commit 3e5191f5c6
parent 9c3818fd98
1 changed files with 103 additions and 0 deletions
--- a/scripts/plotting/consurf_plot.R
+++ b/scripts/plotting/consurf_plot.R
@ -0,0 +1,103 @@
+myColors1 = c("0" = "yellow2"
+             , "1" = "cyan1"
+             , "2" = "steelblue2"
+             , "3" = "cadetblue2"
+             , "4" = "paleturquoise2"
+             , "5" = "thistle3"
+             , "6" = "thistle2"
+             , "7" = "plum2"
+             , "8" = "maroon"
+             , "9" = "violetred2")
+
+
+myColors2 =  c("0" = "yellow2"
+           , "1" = "forestgreen"
+           , "2" = "seagreen3"
+           , "3" = "palegreen1"
+           , "4" = "darkseagreen2"
+           , "5" = "thistle3"
+           , "6" = "lightpink1"
+           , "7" = "orchid3"
+           , "8" = "orchid4"
+           , "9" = "darkorchid4")
+
+
+#myColors <- colorRampPalette(c("cyan", "violetred4"))(9)
+#myColors <- scale_color_brewer(palette = "Cyan-Magenta")
+breaks <- levels(as.factor(mtcars$cyl))
+colours <- ifelse(breaks == 4, "red", "blue")
+
+aa_position_colname  = "position"
+length(unique(merged_df3[[aa_position_colname]]))
+
+positionF <- levels(as.factor(merged_df3[[aa_position_colname]]))
+length(positionF)
+aa_pos_colours = ifelse(positionF%in%rna_bind_aa_pos, "purple"
+                        , ifelse(positionF%in%binding_aa_pos, "orange", "black" ))
+bar = merged_df3
+bar[['lab_bg']] = ifelse(bar[[aa_position_colname]]%in%rna_bind_aa_pos
+                         , "purple"
+                         , ifelse(bar[[aa_position_colname]]%in%binding_aa_pos
+                                  , "orange", "white" ))
+head(bar[[aa_position_colname]])
+head(bar[['lab_bg']])
+
+#bar2 = as.data.frame(cbind(bar[[aa_position]], bar[['lab_bg']])  )
+
+
+
+
+#geom_tile(aes(,-0.8, width = 0.95, height = 0.85)
+#          , fill = df$lab_bg) +
+#geom_tile(aes(,-1.2, width = 0.95, height = -0.2)
+#            , fill = df$lab_bg2) +
+my_xlim = length(unique(bar$position)); my_xlim  
+
+ymin = min(bar$consurf_score)
+ymax = max(bar$consurf_score)
+
+g = ggplot(bar, aes(x = factor(position)
+                       , y =  consurf_score
+                       , colour = factor(consurf_colour_rev))) +   
+  
+  coord_cartesian(xlim = c(1, my_xlim)
+                  , ylim = c(ymin, ymax)
+                  , clip = "off") +
+  geom_point() +  
+  #scale_colour_manual( values = myColors1) +
+  scale_colour_manual( values = myColors2) +
+  geom_errorbar(aes(ymin = consurf_ci_lower, ymax = consurf_ci_upper))
+
+ g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2)
+                       , fill = bar$lab_bg
+                    , colour = "white") 
+ g0
+
+g1 = g0 +  theme( axis.text.x = element_text(size = 10
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4
+                                    #, colour = aa_pos_colours
+                                    )
+         , axis.text.y = element_text(size = 12 
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = 12)
+         , axis.title.y = element_text(size =12 )
+         , panel.background = element_rect(fill = "black", color = "black")
+         , panel.grid.major = element_line(color = "black")
+         , panel.grid.minor = element_line(color = "black")) +
+          guides(colour = guide_legend(title = "Consurf"
+                          , position = "top"
+                          #, direction = "horizontal"
+                          )) +
+  labs(title = ""
+       , x = "Position"
+       , y = "Consurf_score")
+
+g1
+
+
+
+##########################################