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added more scripts

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This commit is contained in:
Tanushree Tunstall 2022-08-24 20:04:29 +01:00
parent 9aed99e805
commit 11b936f09b
9 changed files with 148 additions and 117 deletions
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72
scripts/plotting/plotting_thesis/rpob/prominent_effects_rpob.R
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@ -1,13 +1,11 @@
#!/usr/bin/env Rscript
#source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/rpob.R")
# get plotting dfs
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#=======
# output
#=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
cat("plots will output to:", outdir_images)
########################################################
if (length(merged_df3$position) == length(merged_df3$X5uhc_position) ){
pos_colname = "X5uhc_position"
@ -240,26 +238,32 @@ head(str_df_plot_cols)
# colour based on effect
table(str_df_plot_cols$pe_effect_outcome)
# colors = c("#ffd700" #gold
# , "#f0e68c" #khaki
# , "#da70d6"# orchid
# , "#ff1493"# deeppink
# , "#a0522d" #sienna
# , "#d2b48c" # tan
# , "#00BFC4" #, "#007d85" #blue
# , "#F8766D" )# red
# oops SS should be brighter/darker
# pe_colour_map = c("DD_lig" = "#ffd700" # gold
# , "SS_lig" = "#f0e68c" # khaki
#
# , "DD_nucleic_acid"= "#a0522d" # sienna
# , "SS_nucleic_acid"= "#d2b48c" # sandybrown
#
# , "DD_ppi2" = "#da70d6" # orchid
# , "SS_ppi2" = "#ff1493" # deeppink
#
# , "DD_stability" = "#f8766d" # red
# , "SS_stability" = "#00BFC4") # blue
pe_colour_map = c("DD_lig" = "#ffd700" # gold
, "SS_lig" = "#f0e68c" # khaki
, "DD_nucleic_acid"= "#a0522d" # sienna
, "SS_nucleic_acid"= "#d2b48c" # tan
, "DD_ppi2" = "#da70d6" # orchid
, "SS_ppi2" = "#ff1493" # deeppink
, "DD_stability" = "#f8766d" # red
, "SS_stability" = "#00BFC4") # blue
pe_colour_map = c("DD_lig" = "#f0e68c" # khaki
, "SS_lig" = "#ffd700" # gold
, "DD_nucleic_acid"= "#d2b48c" # sandybrown
, "SS_nucleic_acid"= "#a0522d" # sienna
, "DD_ppi2" = "#da70d6" # orchid
, "SS_ppi2" = "#ff1493" # deeppink
, "DD_stability" = "#f8766d" # red
, "SS_stability" = "#00BFC4") # blue
#unlist(d[c('a', 'a', 'c', 'b')], use.names=FALSE)
@ -320,8 +324,8 @@ if (nrow(ss_lig) == table(str_df_plot_cols$pe_effect_outcome)[['SS_lig']]){
}
#put in chimera cmd
paste0(dd_lig_pos, ".C")
paste0(ss_lig_pos, ".C")
toString(paste0(dd_lig_pos, ".C"))
toString(paste0(ss_lig_pos, ".C"))
#===================================================
#------------------------
@ -344,8 +348,8 @@ if (nrow(ss_nca) == table(str_df_plot_cols$pe_effect_outcome)[['SS_nucleic_acid
}
#put in chimera cmd
paste0(dd_nca_pos, ".C")
paste0(ss_nca_pos, ".C")
toString(paste0(dd_nca_pos, ".C"))
toString(paste0(ss_nca_pos, ".C"))
#===================================================
#-------------------
# PPI2 Affinity
@ -367,8 +371,8 @@ if (nrow(ss_ppi2) == table(str_df_plot_cols$pe_effect_outcome)[['SS_ppi2']]){
}
#put in chimera cmd
paste0(dd_ppi2_pos, ".C")
paste0(ss_ppi2_pos, ".C")
toString(paste0(dd_ppi2_pos, ".C"))
toString(paste0(ss_ppi2_pos, ".C"))
#=========================================================
#------------------------
@ -391,8 +395,8 @@ if (nrow(ss_stability) == table(str_df_plot_cols$pe_effect_outcome)[['SS_stabil
}
#put in chimera cmd
# stabiliting first as it has less numbers
paste0(ss_stability_pos, ".C")
paste0(dd_stability_pos, ".C")
toString(paste0(dd_stability_pos, ".C"))
toString(paste0(ss_stability_pos, ".C"))
####################################################################