added consurf plot function and corresponding test script
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149
scripts/functions/tests/test_consurfP.R
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149
scripts/functions/tests/test_consurfP.R
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## ...opt args
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library(ggplot2)
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library(tidyverse)
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library(cowplot)
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library(gridExtra)
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source("consurf_plot_func.R")
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# ###########################################################################
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# merged_df3 = read.csv("~/git/Data/cycloserine/output/alr_all_params.csv"); source("~/git/LSHTM_analysis/config/alr.R")
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# if ( tolower(gene) == "alr") {
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# aa_pos_lig1 = NULL
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# aa_pos_lig2 = NULL
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# aa_pos_lig3 = NULL
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# p_title = gene
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# }
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###########################################################################
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# merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R")
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# if ( tolower(gene) == "embb") {
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# aa_pos_lig1 = aa_pos_ca
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# aa_pos_lig2 = aa_pos_cdl
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# aa_pos_lig3 = aa_pos_dsl
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# p_title = gene
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# }
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###########################################################################
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# merged_df3 = read.csv("~/git/Data/streptomycin/output/gid_all_params.csv"); source("~/git/LSHTM_analysis/config/gid.R")
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# if ( tolower(gene) == "gid") {
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# aa_pos_lig1 = aa_pos_rna
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# aa_pos_lig2 = aa_pos_sam
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# aa_pos_lig3 = aa_pos_amp
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# p_title = gene
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# }
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###########################################################################
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# merged_df3 = read.csv("~/git/Data/isoniazid/output/katg_all_params.csv"); source("~/git/LSHTM_analysis/config/katg.R")
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# if ( tolower(gene) == "katg") {
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# aa_pos_lig1 = aa_pos_hem
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# aa_pos_lig2 = NULL
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# aa_pos_lig3 = NULL
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# p_title = gene
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# }
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###########################################################################
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# merged_df3 = read.csv("~/git/Data/pyrazinamide/output/pnca_all_params.csv"); source("~/git/LSHTM_analysis/config/pnca.R")
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# if ( tolower(gene) == "pnca") {
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# aa_pos_lig1 = aa_pos_fe
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# aa_pos_lig2 = NULL
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# aa_pos_lig3 = NULL
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# p_title = gene
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# }
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###########################################################################
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merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R")
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if ( tolower(gene) == "rpob") {
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aa_pos_lig1 = NULL
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aa_pos_lig2 = NULL
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aa_pos_lig3 = NULL
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p_title = gene
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}
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#########################################################################
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consurf_palette1 = c("0" = "yellow2"
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, "1" = "cyan1"
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, "2" = "steelblue2"
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, "3" = "cadetblue2"
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, "4" = "paleturquoise2"
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, "5" = "thistle3"
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, "6" = "thistle2"
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, "7" = "plum2"
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, "8" = "maroon"
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, "9" = "violetred2")
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consurf_palette2 = c("0" = "yellow2"
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, "1" = "forestgreen"
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, "2" = "seagreen3"
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, "3" = "palegreen1"
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, "4" = "darkseagreen2"
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, "5" = "thistle3"
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, "6" = "lightpink1"
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, "7" = "orchid3"
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, "8" = "orchid4"
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, "9" = "darkorchid4")
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#################################################
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#active_aa_pos = c(2, 4)
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#aa_pos_drug = c(3, 4, 14, 10)
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aa_pos_hbond = c(2, 4)
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aa_pos_other = c(3, 4, 14, 10)
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wideP_point (plotdf = merged_df3
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, xvar_colname = "position"
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, yvar_colname = "consurf_score"
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, yvar_colourN_colname = "consurf_colour_rev"
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, ylab = "Consurf score"
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, plot_error_bars = F
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, upper_EB_colname = "consurf_ci_upper"
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, lower_EB_colname = "consurf_ci_lower"
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, plot_type = "point"
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, point_colours = consurf_palette2
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, leg_title1 = "Consurf"
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, leg_labels = c("0"="Insufficient Data"
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, "1"= "Variable"
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, "2", "3", "4", "5", "6", "7", "8"
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, "9"= "Conserved")
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# axes title and label sizes
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, x_axts = 8
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, y_axts = 12
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, x_axls = 12
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, y_axls = 15
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, default_xtc = "black"
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, ptitle = p_title
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, xlab = ""
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# x-axis: text colour
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, xtext_colour_aa = F
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, xtext_colour_aa1 = active_aa_pos
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, xtext_colour_aa2 = aa_pos_drug
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, xtext_colours = c("purple", "brown", "black")
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# x-axis: geom tiles ~ lig distance
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, A_xvar_lig = T
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, leg_title2 = "Ligand\nDistance"
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, lig_dist_colname = "ligand_distance"
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, lig_dist_colours = c("green", "yellow", "orange", "red")
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#, tpos0 = 0 #-1.9 #-1.7
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#, tpos0 = 2.5
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#, tW0 = 1
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#, tH0 = 0.2 #0.3
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# x-axis: geom tiles ~ active sites and ligand
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, A_xvar_aa = T
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, active_aa_pos = active_aa_pos
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, active_aa_colour = "brown"
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, aa_pos_drug = aa_pos_drug
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, drug_aa_colour = "purple"
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, aa_pos_lig1 = aa_pos_lig1
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, aa_colour_lig1 = "blue"
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#, tpos1 = 2 #-0.4-1.7 #-0.3-1.65
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, aa_pos_lig2 = aa_pos_lig2
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, aa_colour_lig2 = "cyan"
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#, tpos2 = 1.5#-0.3-1.7 #-0.2-1.65
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, aa_pos_lig3 = aa_pos_lig3
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, aa_colour_lig3 = "cornflowerblue"
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#, tpos3 = 1 #-0.2-1.7#-0.1-1.65
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, default_gt_clr = "white"
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)
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