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This commit is contained in:
Tanushree Tunstall 2022-03-02 11:44:04 +00:00
parent 2274f01f23
commit 6c6709e41e
6 changed files with 198 additions and 29 deletions
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36
scripts/functions/tests/test_consurfP.R
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@ -15,13 +15,13 @@ source("~/git/LSHTM_analysis/scripts/functions/consurfP.R")
# 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/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") {
@ -47,13 +47,13 @@ if ( tolower(gene) == "embb") {
# 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
# }
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"
@ -99,15 +99,19 @@ wideP_consurf(plotdf = merged_df3
, "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
, x_axts = 8
, y_axts = 12
, x_axls = 12
, y_axls = 15
, default_xtc = "black"
, ptitle = p_title
, xlab = ""
, xlab = "" # ylab is above
, pts = 20
# x-axis: text colour
, xtext_colour_aa = F