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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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29
scripts/plotting/plotting_thesis/alr/pe_sens_site_count_alr.R
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@ -3,26 +3,25 @@ source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/sensi
##############################################################
# PE count
#lig-- na--ppi2--stab
# 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
table(str_df_plot_cols$pe_effect_outcome)
##############################################################
#===========
#PE count
#PE count: lig, ppi2, stab
#===========
rects <- data.frame(x=1:6,
colors = c("#ffd700" ,
"#f0e68c" ,
colors = c("#f0e68c" ,
"#ffd700" ,
"#da70d6" ,
"#ff1493" ,

22
scripts/plotting/plotting_thesis/alr/prominent_effects_alr.R
View file

@ -261,6 +261,8 @@ if (nrow(dd_lig) == table(str_df_plot_cols$pe_effect_outcome)[['DD_lig']]){
dd_lig_pos = dd_lig[[pos_colname]]
}else{
stop("Abort: DD affinity colour numbers mismtatch")
print(toString(paste0(dd_lig_pos, chain_suffix)))
}
# +ve Lig Aff
@ -272,13 +274,9 @@ if (!empty(ss_lig)){
stop("Abort: SS affinity colour numbers mismtatch")
}
#put in chimera cmd
paste0(dd_lig_pos, chain_suffix)
paste0(ss_lig_pos, chain_suffix)
print(toString(paste0(ss_lig_pos, chain_suffix)))
}
#===================================================
#-------------------
# PPI2 Affinity
@ -289,6 +287,8 @@ if (nrow(dd_ppi2) == table(str_df_plot_cols$pe_effect_outcome)[['DD_ppi2']]){
dd_ppi2_pos = dd_ppi2[[pos_colname]]
}else{
stop("Abort: DD PPI2 colour numbers mismtatch")
print(toString(paste0(dd_ppi2_pos,chain_suffix)))
}
# +ve PPI2
@ -297,11 +297,11 @@ if (nrow(ss_ppi2) == table(str_df_plot_cols$pe_effect_outcome)[['SS_ppi2']]){
ss_ppi2_pos = ss_ppi2[[pos_colname]]
}else{
stop("Abort: SS PPI2 colour numbers mismtatch")
print(toString(paste0(ss_ppi2_pos,chain_suffix)))
}
#put in chimera cmd
paste0(dd_ppi2_pos,chain_suffix)
paste0(ss_ppi2_pos,chain_suffix)
#=========================================================
#------------------------
@ -323,9 +323,9 @@ if (nrow(ss_stability) == table(str_df_plot_cols$pe_effect_outcome)[['SS_stabil
stop("Abort: SS Stability colour numbers mismtatch")
}
#put in chimera cmd
# stabiliting first as it has less numbers
paste0(ss_stability_pos, chain_suffix)
paste0(dd_stability_pos, chain_suffix)
# put in chimera cmd
print(toString(paste0(dd_stability_pos, chain_suffix)))
print(toString(paste0(ss_stability_pos, chain_suffix)))
####################################################################