tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

various changes

Browse source
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
Download patch file Download diff file Expand all files Collapse all files

5
scripts/Header_TT.R
View file

@ -48,6 +48,11 @@ if (!require("shinyBS")) {
library(shinyBS) library(shinyBS)
} }
if (!require("shinydashboard")) {
install.packages("shinydashboard", dependencies = TRUE)
library(shinydashboard)
}
if (!require("gridExtra")) { if (!require("gridExtra")) {
install.packages("gridExtra", dependencies = TRUE) install.packages("gridExtra", dependencies = TRUE)
library(gridExtra) library(gridExtra)

93
scripts/functions/bp_lineage_diversity.R Normal file
View file

@ -0,0 +1,93 @@
########################################
# Lineage barplot
# Lineage and nsSNP count barplot
# Lineage Diversity barplot
########################################
lin_count_bp_diversity <- function( lf_data = lin_wf
, x_categ = "sel_lineages"
, y_count = "snp_diversity"
#, bar_fill_categ = "count_categ"
, display_label_col = "snp_diversity_f"
, bar_stat_stype = "identity"
, x_lab_angle = 90
, d_lab_size = 5
, d_lab_hjust = 0.5
, d_lab_vjust = 0.5
, d_lab_col = "black"
, my_xats = 20 # x axis text size
, my_yats = 20 # y axis text size
, my_xals = 22 # x axis label size
, my_yals = 22 # y axis label size
, my_lls = 22 # legend label size
, bar_col_labels = c("Mutations", "Total Samples")
, bar_col_values = c("grey50", "gray75")
, bar_leg_name = ""
, leg_location = "top"
, y_log10 = FALSE
, y_scale_percent = FALSE
#, y_label = c("Count", "SNP diversity")
, y_label = c("SNP diversity")
) {
g = ggplot(lf_data
, aes( x = factor( eval(parse(text = x_categ)), ordered = T )
, y = eval(parse(text = y_count))
#, fill = eval(parse(text = bar_fill_categ))
) )
OutPlot = g + geom_bar( stat = bar_stat_stype
, position = position_stack(reverse = TRUE)
#, alpha = 1
#, colour = "grey75"
) +
theme(axis.text.x = element_text(size = my_xats
, angle = x_lab_angle)
, axis.text.y = element_text(size = my_yats
, angle = 90
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_xals
, colour = "black")
, axis.title.y = element_text(size = my_yals
, colour = "black")
, legend.position = leg_location
, legend.text = element_text(size = my_lls)) +
geom_label(aes(label = eval(parse(text = display_label_col)))
, size = d_lab_size
, hjust = d_lab_hjust
, vjust = d_lab_vjust
, colour = d_lab_col
, show.legend = FALSE
#, check_overlap = TRUE
, position = position_stack(reverse = T)) +
scale_fill_manual(values = bar_col_values
, name = bar_leg_name
, labels = bar_col_labels) +
labs(title = ""
, x = ""
, y = y_label
, colour = "black")
if (y_log10){
OutPlot = OutPlot +
scale_y_continuous(trans = "log10"
, labels = trans_format("log10", math_format(10^.x) ) )
}
if (y_scale_percent){
OutPlot = OutPlot +
scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
#scale_y_continuous(labels = scales::percent) +
labs(title = ""
, x = ""
, y = y_label
, colour = "black")
}
return(OutPlot)
}

13
scripts/functions/consurfP.R
View file

@ -28,6 +28,8 @@ wideP_consurf <- function(plotdf
, "1": "Variable" , "1": "Variable"
, "2", "3", "4", "5", "6", "7", "8" , "2", "3", "4", "5", "6", "7", "8"
, "9": "Conserved") , "9": "Conserved")
, panel_col = "black"
, panel_col_fill = "black"
# axes title and label sizes # axes title and label sizes
, x_axls = 12 # x-axis label size , x_axls = 12 # x-axis label size
@ -38,6 +40,7 @@ wideP_consurf <- function(plotdf
, ptitle = "" , ptitle = ""
, xlab = "" , xlab = ""
, ylab = "" , ylab = ""
, pts = 20
# plot margins # plot margins
, t_margin = 0.5 , t_margin = 0.5
@ -282,9 +285,11 @@ wideP_consurf <- function(plotdf
, vjust = 0) , vjust = 0)
, axis.title.x = element_text(size = x_axls) , axis.title.x = element_text(size = x_axls)
, axis.title.y = element_text(size = y_axls ) , axis.title.y = element_text(size = y_axls )
, panel.background = element_rect(fill = "black", color = "black") , panel.background = element_rect(fill = panel_col_fill, color = panel_col)
, panel.grid.major = element_line(color = "black") , panel.grid.major = element_line(color = "black")
, panel.grid.minor = element_line(color = "black") , panel.grid.minor = element_line(color = "black")
, plot.title = element_text(size = pts
, hjust = 0.5)
, plot.margin = margin(t = t_margin , plot.margin = margin(t = t_margin
, r = r_margin , r = r_margin
, b = b_margin , b = b_margin
@ -400,8 +405,6 @@ wideP_consurf <- function(plotdf
out = g1 out = g1
} }
##################################################### #####################################################
# #============================================ # #============================================
# # x-axis: geom_tiles ~ ligand distance # # x-axis: geom_tiles ~ ligand distance
@ -548,13 +551,13 @@ wideP_consurf <- function(plotdf
, legend2 , legend2
, ncol = 1 , ncol = 1
, align = "hv" , align = "hv"
, rel_heights = c(3/4,1)) , rel_heights = c(2/4,3/4))
out2 = cowplot::plot_grid( out + theme(legend.position = "none") out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legs , legs
, ncol = 2 , ncol = 2
, align = "hv" , align = "hv"
, rel_widths = c(9/10, 0.5/10) , rel_widths = c(9/10, 0.4/10)
) )
}else{ }else{
out2 = cowplot::plot_grid( out + theme(legend.position = "none") out2 = cowplot::plot_grid( out + theme(legend.position = "none")

63
scripts/functions/tests/data_for_testingF.R Normal file
View file

@ -0,0 +1,63 @@
############################################################################
# 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
# }
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###########################################################################
# 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
# }
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###########################################################################
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
}
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###########################################################################
# 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
# }
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###########################################################################
# 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
# }
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###########################################################################
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
}
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#########################################################################

34
scripts/functions/tests/test_consurfP.R
View file

@ -15,13 +15,13 @@ source("~/git/LSHTM_analysis/scripts/functions/consurfP.R")
# p_title = gene # p_title = gene
# } # }
########################################################################### ###########################################################################
merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R") # merged_df3 = read.csv("~/git/Data/ethambutol/output/embb_all_params.csv"); source("~/git/LSHTM_analysis/config/embb.R")
if ( tolower(gene) == "embb") { # if ( tolower(gene) == "embb") {
aa_pos_lig1 = aa_pos_ca # aa_pos_lig1 = aa_pos_ca
aa_pos_lig2 = aa_pos_cdl # aa_pos_lig2 = aa_pos_cdl
aa_pos_lig3 = aa_pos_dsl # aa_pos_lig3 = aa_pos_dsl
p_title = gene # p_title = gene
} # }
########################################################################### ###########################################################################
# merged_df3 = read.csv("~/git/Data/streptomycin/output/gid_all_params.csv"); source("~/git/LSHTM_analysis/config/gid.R") # merged_df3 = read.csv("~/git/Data/streptomycin/output/gid_all_params.csv"); source("~/git/LSHTM_analysis/config/gid.R")
# if ( tolower(gene) == "gid") { # if ( tolower(gene) == "gid") {
@ -47,13 +47,13 @@ if ( tolower(gene) == "embb") {
# p_title = gene # p_title = gene
# } # }
########################################################################### ###########################################################################
# merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R") merged_df3 = read.csv("~/git/Data/rifampicin/output/rpob_all_params.csv"); source("~/git/LSHTM_analysis/config/rpob.R")
# if ( tolower(gene) == "rpob") { if ( tolower(gene) == "rpob") {
# aa_pos_lig1 = NULL aa_pos_lig1 = NULL
# aa_pos_lig2 = NULL aa_pos_lig2 = NULL
# aa_pos_lig3 = NULL aa_pos_lig3 = NULL
# p_title = gene p_title = gene
# } }
######################################################################### #########################################################################
consurf_palette1 = c("0" = "yellow2" consurf_palette1 = c("0" = "yellow2"
@ -99,6 +99,8 @@ wideP_consurf(plotdf = merged_df3
, "1" = "Variable" , "1" = "Variable"
, "2", "3", "4", "5", "6", "7", "8" , "2", "3", "4", "5", "6", "7", "8"
, "9" = "Conserved") , "9" = "Conserved")
, panel_col = "black"
, panel_col_fill = "black"
# axes title and label sizes # axes title and label sizes
, x_axts = 8 , x_axts = 8
@ -107,7 +109,9 @@ wideP_consurf(plotdf = merged_df3
, y_axls = 15 , y_axls = 15
, default_xtc = "black" , default_xtc = "black"
, ptitle = p_title , ptitle = p_title
, xlab = "" , xlab = "" # ylab is above
, pts = 20
# x-axis: text colour # x-axis: text colour
, xtext_colour_aa = F , xtext_colour_aa = F

17
scripts/functions/tests/test_logo_plots.R
View file

@ -16,10 +16,10 @@ LP1<- LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position" , x_axis_colname = "position"
, y_axis_colname = "or_mychisq" , y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type" , symbol_colname = "mutant_type"
, y_axis_log = T , y_axis_log = F
, log_value = log10 , log_value = log10
, y_axis_increment = 100 , y_axis_increment = 50
, rm_empty_y = T , rm_empty_y = F
, my_logo_col = 'chemistry' , my_logo_col = 'chemistry'
, x_lab = "Wild-type position" , x_lab = "Wild-type position"
, y_lab = "Odds Ratio" , y_lab = "Odds Ratio"
@ -45,7 +45,7 @@ LP2<- LogoPlotSnps(plot_df = merged_df3
, x_axis_colname = "position" , x_axis_colname = "position"
, symbol_mut_colname = "mutant_type" , symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "wild_type" , symbol_wt_colname = "wild_type"
, omit_snp_count = c(1)# can be 0,1, 2, etc.# DD , omit_snp_count = c(0)# can be 0,1, 2, etc.# DD
, my_logo_col = "chemistry" #DD , my_logo_col = "chemistry" #DD
, x_lab = "Wild-type position" , x_lab = "Wild-type position"
, y_lab = "nsSNP count" , y_lab = "nsSNP count"
@ -75,8 +75,9 @@ LP2<- LogoPlotSnps(plot_df = merged_df3
# to select a small dataset: see test_ed_pfm_data.R # to select a small dataset: see test_ed_pfm_data.R
##################################################### #####################################################
LP3<- LogoPlotMSA(msaSeq_mut = msa_seq LP3<- LogoPlotMSA(unified_msa
, msaSeq_wt = wt_seq #msaSeq_mut = msa_seq
#, msaSeq_wt = wt_seq
, logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw") , logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
, EDScore_type = c("log") , EDScore_type = c("log")
, bg_prob = NULL , bg_prob = NULL
@ -90,7 +91,7 @@ LP3<- LogoPlotMSA(msaSeq_mut = msa_seq
#, y_lab_mut #, y_lab_mut
, x_ats = 10 , x_ats = 10
, x_tangle = 90 , x_tangle = 90
, y_ats = 15 , y_ats = 12
, y_tangle = 0 , y_tangle = 0
, x_tts = 13 , x_tts = 13
, y_tts = 13 , y_tts = 13
@ -106,7 +107,7 @@ out_logoP = cowplot::plot_grid(LP3, LP1, LP2
, nrow = 3 , nrow = 3
, ncol = 1 , ncol = 1
, rel_width = c(1/3, 0.5/3, 1/3) , rel_width = c(1/3, 0.5/3, 1/3)
, rel_heights = c(1, 1, 1) , rel_heights = c(0.8/2, 0.5/2, 0.7/2)
, align = "hv") , align = "hv")
out_logoP out_logoP