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corrected the pe colour mapping

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This commit is contained in:
Tanushree Tunstall 2022-08-24 20:55:36 +01:00
parent 11b936f09b
commit 19b820e316
10 changed files with 61 additions and 90 deletions
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14
scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R
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@ -7,21 +7,19 @@
#============= #=============
# Data: Input # Data: Input
#============== #==============
source("~/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/alr.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols)) #cat("\nSourced plotting cols as well:", length(plotting_cols))
####################################################
class(merged_df3)
df3 = subset(merged_df3, select = -c(pos_count))
#======= #=======
# output # output
#======= #=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/") outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
cat("plots will output to:", outdir_images) cat("plots will output to:", outdir_images)
####################################################
class(merged_df3)
df3 = subset(merged_df3, select = -c(pos_count))
########################################################## ##########################################################
# blue, red bp # blue, red bp
sts = 8 sts = 8

22
scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
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@ -3,17 +3,17 @@ source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensi
############################################################## ##############################################################
# PE count # PE count
#pe_colour_map = c("DD_lig" = "#f0e68c" # khaki pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
# , "SS_lig" = "#ffd700" # gold , "SS_lig" = "#ffd700" # gold
# , "DD_nucleic_acid"= "#d2b48c" # sandybrown , "DD_nucleic_acid"= "#d2b48c" # sandybrown
# , "SS_nucleic_acid"= "#a0522d" # sienna , "SS_nucleic_acid"= "#a0522d" # sienna
# , "DD_ppi2" = "#da70d6" # orchid , "DD_ppi2" = "#da70d6" # orchid
# , "SS_ppi2" = "#ff1493" # deeppink , "SS_ppi2" = "#ff1493" # deeppink
# , "DD_stability" = "#f8766d" # red , "DD_stability" = "#f8766d" # red
# , "SS_stability" = "#00BFC4") # blue , "SS_stability" = "#00BFC4") # blue
table(str_df_plot_cols$pe_effect_outcome) table(str_df_plot_cols$pe_effect_outcome)
############################################################## ##############################################################
#=========== #===========

32
scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R
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@ -191,27 +191,17 @@ head(str_df_plot_cols)
# colour based on effect # colour based on effect
table(str_df_plot_cols$pe_effect_outcome) table(str_df_plot_cols$pe_effect_outcome)
# colors = c("#ffd700" #gold pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
# , "#f0e68c" #khaki , "SS_lig" = "#ffd700" # gold
# , "#da70d6"# orchid
# , "#ff1493"# deeppink , "DD_nucleic_acid"= "#d2b48c" # sandybrown
# , "#a0522d" #sienna , "SS_nucleic_acid"= "#a0522d" # sienna
# , "#d2b48c" # tan
# , "#00BFC4" #, "#007d85" #blue , "DD_ppi2" = "#da70d6" # orchid
# , "#F8766D" )# red , "SS_ppi2" = "#ff1493" # deeppink
pe_colour_map = c("DD_lig" = "#ffd700" # gold , "DD_stability" = "#f8766d" # red
, "SS_lig" = "#f0e68c" # khaki , "SS_stability" = "#00BFC4") # blue
, "DD_nucleic_acid"= "#a0522d" # sienna
, "SS_nucleic_acid"= "#d2b48c" # tan
, "DD_ppi2" = "#da70d6" # orchid
, "SS_ppi2" = "#ff1493" # deeppink
, "DD_stability" = "#f8766d" # red
, "SS_stability" = "#00BFC4") # blue
#unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE) #unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE)
#map the colours #map the colours

4
scripts/plotting/plotting_thesis/gid/basic_barplots_gid_layout.R
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@ -2,11 +2,11 @@
# Data: Input # Data: Input
#============== #==============
source("~/git/LSHTM_analysis/config/gid.R") source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols))
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R") source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R") source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/pe_sens_site_count_gid.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols))
#======= #=======
# output # output

33
scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R
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@ -203,27 +203,18 @@ head(str_df_plot_cols)
# colour based on effect # colour based on effect
table(str_df_plot_cols$pe_effect_outcome) table(str_df_plot_cols$pe_effect_outcome)
# colors = c("#ffd700" #gold pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
# , "#f0e68c" #khaki , "SS_lig" = "#ffd700" # gold
# , "#da70d6"# orchid
# , "#ff1493"# deeppink , "DD_nucleic_acid"= "#d2b48c" # sandybrown
# , "#a0522d" #sienna , "SS_nucleic_acid"= "#a0522d" # sienna
# , "#d2b48c" # tan
# , "#00BFC4" #, "#007d85" #blue , "DD_ppi2" = "#da70d6" # orchid
# , "#F8766D" )# red , "SS_ppi2" = "#ff1493" # deeppink
pe_colour_map = c("DD_lig" = "#ffd700" # gold , "DD_stability" = "#f8766d" # red
, "SS_lig" = "#f0e68c" # khaki , "SS_stability" = "#00BFC4") # blue
, "DD_nucleic_acid"= "#a0522d" # sienna
, "SS_nucleic_acid"= "#d2b48c" # tan
, "DD_ppi2" = "#da70d6" # orchid
, "SS_ppi2" = "#ff1493" # deeppink
, "DD_stability" = "#f8766d" # red
, "SS_stability" = "#00BFC4") # blue
#unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE) #unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE)
#map the colours #map the colours

4
scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R
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@ -7,8 +7,8 @@
#============= #=============
# Data: Input # Data: Input
#============== #==============
source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols)) #cat("\nSourced plotting cols as well:", length(plotting_cols))

5
scripts/plotting/plotting_thesis/katg/basic_barplots_katg_layout.R
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@ -1,8 +1,9 @@
#============= #=============
# Data: Input # Data: Input
#============== #==============
#source("~/git/LSHTM_analysis/config/katg.R") source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R") source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R")
source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R") source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R")

2
scripts/plotting/plotting_thesis/katg/pe_sens_site_count_katg.R
View file

@ -3,7 +3,7 @@ source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/katg/sens
############################################################## ##############################################################
# PE count # PE count
#pe_colour_map = c("DD_lig" = "#f0e68c" # khaki #pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
# , "SS_lig" = "#ffd700" # gold # , "SS_lig" = "#ffd700" # gold
# , "DD_nucleic_acid"= "#d2b48c" # sandybrown # , "DD_nucleic_acid"= "#d2b48c" # sandybrown

33
scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R
View file

@ -191,27 +191,18 @@ head(str_df_plot_cols)
# colour based on effect # colour based on effect
table(str_df_plot_cols$pe_effect_outcome) table(str_df_plot_cols$pe_effect_outcome)
# colors = c("#ffd700" #gold pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
# , "#f0e68c" #khaki , "SS_lig" = "#ffd700" # gold
# , "#da70d6"# orchid
# , "#ff1493"# deeppink , "DD_nucleic_acid"= "#d2b48c" # sandybrown
# , "#a0522d" #sienna , "SS_nucleic_acid"= "#a0522d" # sienna
# , "#d2b48c" # tan
# , "#00BFC4" #, "#007d85" #blue , "DD_ppi2" = "#da70d6" # orchid
# , "#F8766D" )# red , "SS_ppi2" = "#ff1493" # deeppink
pe_colour_map = c("DD_lig" = "#ffd700" # gold , "DD_stability" = "#f8766d" # red
, "SS_lig" = "#f0e68c" # khaki , "SS_stability" = "#00BFC4") # blue
, "DD_nucleic_acid"= "#a0522d" # sienna
, "SS_nucleic_acid"= "#d2b48c" # tan
, "DD_ppi2" = "#da70d6" # orchid
, "SS_ppi2" = "#ff1493" # deeppink
, "DD_stability" = "#f8766d" # red
, "SS_stability" = "#00BFC4") # blue
#unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE) #unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE)
#map the colours #map the colours

2
scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R
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@ -252,7 +252,7 @@ table(str_df_plot_cols$pe_effect_outcome)
# , "SS_stability" = "#00BFC4") # blue # , "SS_stability" = "#00BFC4") # blue
pe_colour_map = c("DD_lig" = "#f0e68c" # khaki pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
, "SS_lig" = "#ffd700" # gold , "SS_lig" = "#ffd700" # gold
, "DD_nucleic_acid"= "#d2b48c" # sandybrown , "DD_nucleic_acid"= "#d2b48c" # sandybrown