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This commit is contained in:
Tanushree Tunstall 2022-08-23 21:54:16 +01:00
parent 0284122ef2
commit 9aed99e805
6 changed files with 26 additions and 22 deletions
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2
config/alr.R
View file

@ -144,4 +144,4 @@ aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("ALR","PLP"), tile_map=data.frame(tile=c("ALR","PLP"),
tile_colour=c("green","darkslategrey")) tile_colour=c("green","navyblue")) #darkslategrey

9
config/katg.R
View file

@ -106,6 +106,11 @@ cat("\n==================================================="
aa_pos_lig1 = aa_pos_hem aa_pos_lig1 = aa_pos_hem
aa_pos_lig2 = NULL aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("KAT","DPA","CDL","Ca"), tile_map=data.frame(tile=c("INH","HAEM"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey"))
#toString(aa_pos_hem)
#toString(aa_pos_drug)
#toString(active_aa_pos)

5
scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R
View file

@ -7,9 +7,8 @@
#============= #=============
# Data: Input # Data: Input
#============== #==============
#source("~/git/LSHTM_analysis/config/katg.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))
#################################################### ####################################################

12
scripts/plotting/plotting_thesis/gid/prominent_effects_gid.R
View file

@ -274,6 +274,8 @@ if (nrow(dd_lig) == table(str_df_plot_cols$pe_effect_outcome)[['DD_lig']]){
}else{ }else{
stop("Abort: DD affinity colour numbers mismtatch") stop("Abort: DD affinity colour numbers mismtatch")
} }
paste0(dd_lig_pos,chain_suffix)
toString(paste0(dd_lig_pos,chain_suffix))
# +ve Lig Aff # +ve Lig Aff
ss_lig = str_df_plot_cols[str_df_plot_cols$pe_effect_outcome=="SS_lig",] ss_lig = str_df_plot_cols[str_df_plot_cols$pe_effect_outcome=="SS_lig",]
@ -284,8 +286,8 @@ if (nrow(ss_lig) == table(str_df_plot_cols$pe_effect_outcome)[['SS_lig']]){
stop("Abort: SS affinity colour numbers mismtatch") stop("Abort: SS affinity colour numbers mismtatch")
} }
#put in chimera cmd #put in chimera cmd
paste0(dd_lig_pos,chain_suffix)
paste0(ss_lig_pos,chain_suffix) paste0(ss_lig_pos,chain_suffix)
toString(paste0(ss_lig_pos,chain_suffix))
} }
@ -310,8 +312,8 @@ if (nrow(ss_nca) == table(str_df_plot_cols$pe_effect_outcome)[['SS_nucleic_acid
} }
#put in chimera cmd #put in chimera cmd
paste0(dd_nca_pos, chain_suffix) toString(paste0(dd_nca_pos, chain_suffix))
paste0(ss_nca_pos, chain_suffix) toString(paste0(ss_nca_pos, chain_suffix))
#========================================================= #=========================================================
#------------------------ #------------------------
@ -335,7 +337,7 @@ if (nrow(ss_stability) == table(str_df_plot_cols$pe_effect_outcome)[['SS_stabil
#put in chimera cmd #put in chimera cmd
# stabiliting first as it has less numbers # stabiliting first as it has less numbers
paste0(ss_stability_pos, chain_suffix) toString(paste0(dd_stability_pos, chain_suffix))
paste0(dd_stability_pos, chain_suffix) toString(paste0(ss_stability_pos, chain_suffix))
#################################################################### ####################################################################

4
scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R
View file

@ -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))

16
scripts/plotting/plotting_thesis/katg/prominent_effects_katg.R
View file

@ -262,6 +262,8 @@ if (nrow(dd_lig) == table(str_df_plot_cols$pe_effect_outcome)[['DD_lig']]){
}else{ }else{
stop("Abort: DD affinity colour numbers mismtatch") stop("Abort: DD affinity colour numbers mismtatch")
} }
toString(paste0(dd_lig_pos, chain_suffix))
# +ve Lig Aff # +ve Lig Aff
ss_lig = str_df_plot_cols[str_df_plot_cols$pe_effect_outcome=="SS_lig",] ss_lig = str_df_plot_cols[str_df_plot_cols$pe_effect_outcome=="SS_lig",]
@ -272,13 +274,10 @@ if (!empty(ss_lig)){
stop("Abort: SS affinity colour numbers mismtatch") stop("Abort: SS affinity colour numbers mismtatch")
} }
#put in chimera cmd #put in chimera cmd
paste0(dd_lig_pos, chain_suffix) toString(paste0(ss_lig_pos, chain_suffix))
paste0(ss_lig_pos, chain_suffix)
} }
#=================================================== #===================================================
#------------------- #-------------------
# PPI2 Affinity # PPI2 Affinity
@ -300,8 +299,8 @@ if (nrow(ss_ppi2) == table(str_df_plot_cols$pe_effect_outcome)[['SS_ppi2']]){
} }
#put in chimera cmd #put in chimera cmd
paste0(dd_ppi2_pos,chain_suffix) toString(paste0(dd_ppi2_pos,chain_suffix))
paste0(ss_ppi2_pos,chain_suffix) toString(paste0(ss_ppi2_pos,chain_suffix))
#========================================================= #=========================================================
#------------------------ #------------------------
@ -324,8 +323,7 @@ if (nrow(ss_stability) == table(str_df_plot_cols$pe_effect_outcome)[['SS_stabil
} }
#put in chimera cmd #put in chimera cmd
# stabiliting first as it has less numbers toString(paste0(dd_stability_pos, chain_suffix))
paste0(ss_stability_pos, chain_suffix) toString(paste0(ss_stability_pos, chain_suffix))
paste0(dd_stability_pos, chain_suffix)
#################################################################### ####################################################################