153 lines
5.6 KiB
R
153 lines
5.6 KiB
R
|
|
## ...opt args
|
|
library(ggplot2)
|
|
library(tidyverse)
|
|
library(cowplot)
|
|
library(gridExtra)
|
|
source("~/git/LSHTM_analysis/scripts/functions/consurfP.R")
|
|
|
|
############################################################################
|
|
# merged_df3 = read.csv("~/git/Data/cycloserine/output/alr_all_params.csv"); source("~/git/LSHTM_analysis/config/alr.R")
|
|
# if ( tolower(gene) == "alr") {
|
|
# aa_pos_lig1 = NULL
|
|
# aa_pos_lig2 = NULL
|
|
# aa_pos_lig3 = NULL
|
|
# p_title = gene
|
|
# }
|
|
###########################################################################
|
|
# merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R")
|
|
# if ( tolower(gene) == "embb") {
|
|
# aa_pos_lig1 = aa_pos_ca
|
|
# aa_pos_lig2 = aa_pos_cdl
|
|
# aa_pos_lig3 = aa_pos_dsl
|
|
# p_title = gene
|
|
# }
|
|
###########################################################################
|
|
# merged_df3 = read.csv("~/git/Data/streptomycin/output/gid_all_params.csv"); source("~/git/LSHTM_analysis/config/gid.R")
|
|
# if ( tolower(gene) == "gid") {
|
|
# aa_pos_lig1 = aa_pos_rna
|
|
# aa_pos_lig2 = aa_pos_sam
|
|
# aa_pos_lig3 = aa_pos_amp
|
|
# p_title = gene
|
|
# }
|
|
###########################################################################
|
|
# merged_df3 = read.csv("~/git/Data/isoniazid/output/katg_all_params.csv"); source("~/git/LSHTM_analysis/config/katg.R")
|
|
# if ( tolower(gene) == "katg") {
|
|
# aa_pos_lig1 = aa_pos_hem
|
|
# aa_pos_lig2 = NULL
|
|
# aa_pos_lig3 = NULL
|
|
# p_title = gene
|
|
# }
|
|
###########################################################################
|
|
# merged_df3 = read.csv("~/git/Data/pyrazinamide/output/pnca_all_params.csv"); source("~/git/LSHTM_analysis/config/pnca.R")
|
|
# if ( tolower(gene) == "pnca") {
|
|
# aa_pos_lig1 = aa_pos_fe
|
|
# aa_pos_lig2 = NULL
|
|
# aa_pos_lig3 = NULL
|
|
# p_title = gene
|
|
# }
|
|
###########################################################################
|
|
merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R")
|
|
if ( tolower(gene) == "rpob") {
|
|
aa_pos_lig1 = NULL
|
|
aa_pos_lig2 = NULL
|
|
aa_pos_lig3 = NULL
|
|
p_title = gene
|
|
}
|
|
#########################################################################
|
|
|
|
consurf_palette1 = c("0" = "yellow2"
|
|
, "1" = "cyan1"
|
|
, "2" = "steelblue2"
|
|
, "3" = "cadetblue2"
|
|
, "4" = "paleturquoise2"
|
|
, "5" = "thistle3"
|
|
, "6" = "thistle2"
|
|
, "7" = "plum2"
|
|
, "8" = "maroon"
|
|
, "9" = "violetred2")
|
|
|
|
consurf_palette2 = c("0" = "yellow2"
|
|
, "1" = "forestgreen"
|
|
, "2" = "seagreen3"
|
|
, "3" = "palegreen1"
|
|
, "4" = "darkseagreen2"
|
|
, "5" = "thistle3"
|
|
, "6" = "lightpink1"
|
|
, "7" = "orchid3"
|
|
, "8" = "orchid4"
|
|
, "9" = "darkorchid4")
|
|
|
|
#################################################
|
|
#active_aa_pos = c(2, 4)
|
|
#aa_pos_drug = c(3, 4, 14, 10)
|
|
aa_pos_hbond = c(2, 4)
|
|
aa_pos_other = c(3, 4, 14, 10)
|
|
|
|
wideP_consurf(plotdf = merged_df3
|
|
, xvar_colname = "position"
|
|
, yvar_colname = "consurf_score"
|
|
, yvar_colourN_colname = "consurf_colour_rev"
|
|
, ylab = "Consurf score"
|
|
, plot_error_bars = T
|
|
, upper_EB_colname = "consurf_ci_upper"
|
|
, lower_EB_colname = "consurf_ci_lower"
|
|
, plot_type = "point"
|
|
, point_colours = consurf_palette2
|
|
, leg_title1 = "Consurf"
|
|
, leg_labels = c("0"="Insufficient Data"
|
|
, "1" = "Variable"
|
|
, "2", "3", "4", "5", "6", "7", "8"
|
|
, "9" = "Conserved")
|
|
, panel_col = "black"
|
|
, panel_col_fill = "black"
|
|
|
|
# axes title and label sizes
|
|
, x_axts = 8
|
|
, y_axts = 12
|
|
, x_axls = 12
|
|
, y_axls = 15
|
|
, default_xtc = "black"
|
|
, ptitle = p_title
|
|
, xlab = "" # ylab is above
|
|
, pts = 20
|
|
|
|
|
|
# x-axis: text colour
|
|
, xtext_colour_aa = F
|
|
, xtext_colour_aa1 = active_aa_pos
|
|
, xtext_colour_aa2 = aa_pos_drug
|
|
, xtext_colours = c("purple", "brown", "black")
|
|
|
|
# x-axis: geom tiles ~ lig distance
|
|
, A_xvar_lig = T
|
|
, leg_title2 = "Ligand\nDistance"
|
|
, lig_dist_colname = "ligand_distance"
|
|
, lig_dist_colours = c("green", "yellow", "orange", "red")
|
|
#, tpos0 = 0 #-1.9 #-1.7
|
|
#, tpos0 = 2.5
|
|
#, tW0 = 1
|
|
#, tH0 = 0.2 #0.3
|
|
|
|
# x-axis: geom tiles ~ active sites and ligand
|
|
, A_xvar_aa = T
|
|
, active_aa_pos = active_aa_pos
|
|
, active_aa_colour = "brown"
|
|
, aa_pos_drug = aa_pos_drug
|
|
, drug_aa_colour = "purple"
|
|
|
|
, aa_pos_lig1 = aa_pos_lig1
|
|
, aa_colour_lig1 = "blue"
|
|
#, tpos1 = 2 #-0.4-1.7 #-0.3-1.65
|
|
|
|
, aa_pos_lig2 = aa_pos_lig2
|
|
, aa_colour_lig2 = "cyan"
|
|
#, tpos2 = 1.5#-0.3-1.7 #-0.2-1.65
|
|
|
|
, aa_pos_lig3 = aa_pos_lig3
|
|
, aa_colour_lig3 = "cornflowerblue"
|
|
#, tpos3 = 1 #-0.2-1.7#-0.1-1.65
|
|
|
|
, default_gt_clr = "white"
|
|
|
|
)
|