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gene_vulnerability_comparison_plots.R
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gene_vulnerability_comparison_plots.R
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# Vulnerability modeling - parallel
# Imports ----
source("vulnerability_modeling_tools.R")
source("vulnerability_plotting_tools.R")
get_data = function(gene, exp, strain, date, basedir){
sample_path = get_gene_samples_path(gene, label=strain, basedir=basedir)
model_data_path = get_gene_model_data_path(gene, label=strain, basedir=basedir)
if(file.exists(sample_path) & file.exists(model_data_path)) {
fit_samples = read.csv(sample_path, comment.char="#")
model_data = readRDS(model_data_path)
model_data[["gene"]] = gene
model_data[["strain"]] = strain
} else {
fit_samples = NULL
model_data = NULL
}
return(list(fit_samples=fit_samples, model_data=model_data))
}
plot_comparisons_parallel_helper = function(comparison,
summary_color = c("#262626", "#A86487", "#D55E00", "blue"),
summary_size= c(3, 3, 3, 3),
summary_alpha= c(1, 1, 1, 1),
# Bands
band_color = c("#262626", "#A86487", "#D55E00", "blue"),
band_size= c(1, 1, 1, 1),
band_alpha = c(0.02, 0.02, 0.02, 0.02),
band_style="lines",
# Dot
dot_color = c("#262626", "#A86487", "#D55E00", "blue"),
dot_size= c(1, 1, 1, 1),
dot_alpha= c(1, 1, 1, 1),
dot_style = "both",
# Summary
hist_color = c("#262626", "#008B8B", "#D55E00", "blue"),
hist_size= c(3, 3, 3, 3),
hist_alpha= c(0.2, 0.2, 0.2, 0.2),
# Bands
border_color = c("black", "#609393", "#D55E00", "blue"),
border_size= c(1, 1, 1, 1),
border_alpha = c(0.02, 0.02, 0.02, 0.02),
width=13, height=10,
samples=1000, str_resolution = 0.01,
include_gamma=TRUE, include_legend=TRUE,
target="beta_e",
y_min=NULL, y_max=NULL,
breaks=NULL, format="png",
ylab="", xlab="", safe=FALSE
){
encountered_error = FALSE
label_list = c()
N_comp = length(comparison)
for(i in 1:N_comp){
temp_A = temp_A = get_data(comparison[[i]]$gene, comparison[[i]]$exp, comparison[[i]]$strain, comparison[[i]]$date, comparison[[i]]$dir)
fit_samples_A = temp_A$fit_samples
model_data_A = temp_A$model_data
if(!is.null(fit_samples_A)) {
if (!"beta_min" %in% colnames(fit_samples_A)){
fit_samples_A["beta_min"] = 0
}
comparison[[i]][["fit_samples"]] = fit_samples_A
comparison[[i]][["model_data"]] = model_data_A
labelA = paste0(comparison[[i]]$strain, "_", gsub(":", "_", comparison[[i]]$gene))
label_list = c(label_list, labelA)
} else {
encountered_error = TRUE
}
}
# temp_B = temp_A = get_data(comparison[[2]]$gene, comparison[[2]]$exp, comparison[[2]]$strain, comparison[[2]]$date, opt$dir)
# fit_samples_B = temp_B$fit_samples
# model_data_B = temp_B$model_data
# comparison[[2]][["fit_samples"]] = fit_samples_B
# comparison[[2]][["model_data"]] = model_data_B
#
full_label = paste(label_list, collapse = "_")
# Beta_E
dir.create(file.path(output_prefix, "beta_e_logistic_fits"), showWarnings = FALSE, recursive=TRUE)
output_path = file.path(output_prefix, "beta_e_logistic_fits",
paste("plot_beta_e_logistic_fit_",
full_label, ".", format, sep=""))
if(!file.exists(output_path) | !safe) {
#message("output_path did not exist", output_path, exists(output_path), " or not safe", !safe)
result = tryCatch({
plot_multiple_fits(comparison, output_path,
summary_color = summary_color,
summary_size = summary_size,
summary_alpha = summary_alpha,
# Bands
band_color = band_color,
band_size = band_size,
band_alpha = band_alpha,
band_style = band_style,
# Dot
dot_color = dot_color,
dot_size = dot_size,
dot_alpha = dot_alpha,
dot_style = dot_style,
width=width, height=height,
samples=samples, str_resolution = str_resolution,
include_gamma=include_gamma, include_legend=include_legend,
target=target,
y_min=y_min, y_max=y_max, breaks=breaks)
}, error = function(e) {
sample_path = get_gene_samples_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
model_data_path = get_gene_model_data_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
message("Error plotting\n\t", output_path, "\n\t", sample_path, "\n\t", model_data_path, "\n")
message("\n\t ", e)
encountered_error = TRUE
})
} else {message("File already exists and being safe. Skipping ", output_path)}
dir.create(file.path(output_prefix, "predlogFC_logistic_fits"), showWarnings = FALSE, recursive=TRUE)
output_path = file.path(output_prefix, "predlogFC_logistic_fits",
paste("plot_predlogFC_logistic_fit_",
full_label, ".", format, sep=""))
if(!file.exists(output_path) | !safe) {
result = tryCatch({
plot_multiple_fits(comparison, output_path,
summary_color = summary_color,
summary_size = summary_size,
summary_alpha = summary_alpha,
# Bands
band_color = band_color,
band_size = band_size,
band_alpha = band_alpha,
band_style = band_style,
# Dot
dot_color = dot_color,
dot_size = dot_size,
dot_alpha = dot_alpha,
dot_style = dot_style,
width=width, height=height,
samples=samples, str_resolution = str_resolution,
include_gamma=FALSE, include_legend=include_legend,
target="predlogFC",
y_min=y_min, y_max=y_max, breaks=breaks)
}, error = function(e) {
sample_path = get_gene_samples_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
model_data_path = get_gene_model_data_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
message("Error plotting\n\t", output_path, "\n\t", sample_path, "\n\t", model_data_path, "\n")
message("\n\t ", e)
encountered_error = TRUE
})
} else {message("File already exists and being safe. Skipping ", output_path)}
# Fmin histograms
dir.create(file.path(output_prefix, "Fmin_histograms"), showWarnings = FALSE, recursive=TRUE)
output_path = file.path(output_prefix, "Fmin_histograms",
paste("plot_Fmin_histograms_",
full_label, ".", format, sep=""))
if(!file.exists(output_path) | !safe) {
result = tryCatch({
plot_multiple_Fmin_histograms(comparison, output_path,
# Summary
hist_color = hist_color,
hist_size= hist_size,
hist_alpha= hist_alpha,
# Bands
border_color = border_color,
border_size= border_size,
border_alpha = border_alpha,
border_style="lines",
# Misc
width=10, height=10,
samples=1000, str_resolution = 0.01,
x_min=NULL, x_max=NULL,
x_label="Fmin",
bins = 150,
hdi=TRUE)
}, error = function(e) {
sample_path = get_gene_samples_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
model_data_path = get_gene_model_data_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
message("Error plotting\n\t", output_path, "\n\t", sample_path, "\n\t", model_data_path, "\n")
message("\n\t ", e)
encountered_error = TRUE
})
} else {message("File already exists and being safe. Skipping ", output_path)}
#dir.create(file.path(output_prefix, "vulnerability_histograms"), showWarnings = FALSE, recursive=TRUE)
#output_path = file.path(output_prefix, "vulnerability_histograms",
# paste("plot_vulnerability_histograms_",
# full_label, ".", format, sep=""))
#result = tryCatch({
# plot_multiple_vulnerability_histograms(comparison, output_path,
# # Summary
# hist_color = c("#262626", "#008B8B", "#D55E00", "blue"),
# hist_size= c(3, 3, 3, 3),
# hist_alpha= c(0.2, 0.2, 0.2, 0.2),
#
# # Bands
# border_color = c("black", "#609393", "#D55E00", "blue"),
# # border_color = c("red", "blue", "#D55E00", "blue"),
# border_size= c(1, 1, 1, 1),
# border_alpha = c(0.02, 0.02, 0.02, 0.02),
# border_style="lines",
#
# # Misc
# width=10, height=10,
# samples=1000, str_resolution = 0.01,
# include_gamma=TRUE, target="beta_e",
# x_min=NULL, x_max=NULL,
# x_label="Vulnerability",
# breaks=c(0.0, -0.2, -0.4, -0.6, -0.8, -1.0),
# bins = 150
# )
#
#}, error = function(e) {
#
# sample_path = get_gene_samples_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
# model_data_path = get_gene_model_data_path(comparison[[1]]$gene, label=comparison[[1]]$strain, basedir=comparison[[1]]$dir)
# message("Error plotting\n\t", output_path, "\n\t", sample_path, "\n\t", model_data_path, "\n")
# message("\n\t ", e)
#})
return (encountered_error)
}
require("optparse")
# Options ----
Sys.setenv(LOCAL_CPPFLAGS = '-march=corei7 -mtune=corei7')
options(mc.cores = parallel::detectCores())
# Main ----
args = commandArgs(trailingOnly=TRUE)
# test if there is at least one argument: if not, return an error
option_list = list(
# Data stuff:
make_option("--strain1", type="character", default="",
help="Strain for condition 1. Used as reference."),
make_option("--exp1", type="character", default="",
help="Exp for condition 1."),
make_option("--date1", type="character", default="",
help="Date for condition 1."),
make_option("--label1", type="character", default="",
help="label for the condition1."),
make_option("--data1", type="character", default="",
help="Data for condition 1."),
make_option("--dir1", type="character", default="./",
help="Base data dir for condition 1"),
make_option("--strain2", type="character", default="",
help="Strain for condition 2. Used as reference."),
make_option("--exp2", type="character", default="",
help="Exp for condition 2."),
make_option("--date2", type="character", default="",
help="Date for condition 2."),
make_option("--label2", type="character", default="",
help="label for the condition 2."),
make_option("--data2", type="character", default="",
help="Data for condition 2."),
make_option("--dir2", type="character", default="./",
help="Base data dir for condition 2"),
make_option("--plot_dir", type="character", default="./",
help="Base dir to output plots"),
make_option("--genes", type="character", default="",
help="Gene path"),
#System stuff:
make_option("--cores", type="numeric", default=15,
help="Number of cores to use"),
# plotting stuff:
make_option("--ymax", type="numeric", default=0.05,
help="Max value for the y-axis"),
make_option("--ymin", type="numeric", default=-1.0,
help="minimum for the y-axis"),
make_option("--xlab", type="character", default="",
help="Label to use for the x-axis"),
make_option("--ylab", type="character", default="",
help="Label to use for the y-axis"),
# SUMMARY
make_option("--summary_color1", type="character", default="#262626",
help="Color for the summary"),
make_option("--summary_alpha1", type="numeric", default=1,
help="Alpha for the summary"),
make_option("--summary_size1", type="numeric", default=3,
help="Size for the summary"),
make_option("--summary_color2", type="character", default="#A86487",
help="Color for the summary"),
make_option("--summary_alpha2", type="numeric", default=1,
help="Alpha for the summary"),
make_option("--summary_size2", type="numeric", default=3,
help="Size for the summary"),
# BANDS
make_option("--band_color1", type="character", default="#AAAAAA",
help="Color for the band"),
make_option("--band_alpha1", type="numeric", default=0.1,
help="Alpha for the band"),
make_option("--band_size1", type="numeric", default=1,
help="Size for the band"),
make_option("--band_color2", type="character", default="#845B86",
help="Color for the band"),
make_option("--band_alpha2", type="numeric", default=0.1,
help="Alpha for the band"),
make_option("--band_size2", type="numeric", default=1,
help="Size for the band"),
# DOTS
make_option("--dot_color1", type="character", default="#262626",
help="Color for the dots"),
make_option("--dot_alpha1", type="numeric", default=0.9,
help="Alpha for the dots"),
make_option("--dot_size1", type="numeric", default=2,
help="Size for the dots"),
make_option("--dot_color2", type="character", default="#A86487",
help="Color for the dots"),
make_option("--dot_alpha2", type="numeric", default=0.9,
help="Alpha for the dots"),
make_option("--dot_size2", type="numeric", default=2,
help="Size for the dots"),
# Histograms
make_option("--hist_color1", type="character", default="#878787",
help="Color for the histogram bars"),
make_option("--hist_size1", type="numeric", default=2,
help="Size for the histogram bars"),
make_option("--hist_alpha1", type="numeric", default=0.7,
help="Alpha for the histogram bars"),
make_option("--border_color1", type="character", default="#676767",
help="Color for the histogram border"),
make_option("--border_size1", type="numeric", default=2,
help="Size for the histogram border"),
make_option("--border_alpha1", type="numeric", default=0.7,
help="Alpha for the histogram border"),
make_option("--hist_color2", type="character", default="#AA86AC",
help="Color for the histogram bars"),
make_option("--hist_size2", type="numeric", default=2,
help="Size for the histogram bars"),
make_option("--hist_alpha2", type="numeric", default=0.7,
help="Alpha for the histogram bars"),
make_option("--border_color2", type="character", default="#845B86",
help="Color for the histogram border"),
make_option("--border_size2", type="numeric", default=2,
help="Size for the histogram border"),
make_option("--border_alpha2", type="numeric", default=0.7,
help="Alpha for the histogram border"),
make_option("--format", type="character", default="png",
help="Output format"),
make_option("--width", type="numeric", default=13,
help="Width of plots"),
make_option("--height", type="numeric", default=10,
help="Width of plots"),
make_option("--band_style", type="character", default="lines",
help="Type of band to use"),
make_option("--dot_style", type="character", default="both",
help="Type of dots to use"),
make_option("--hide_legend", action="store_true", default=FALSE,
help="Hide legend"),
make_option("--hide_gamma", action="store_true", default=FALSE,
help="Hide gamma"),
make_option("--safe", action="store_true", default=FALSE,
help="Don't overwrite existing plots")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
#
# if(FALSE){
# opt = list(strain1="H37Rv", exp1="biotinRS", date1="03_20_2023",
# data1="/store/home/mad/vulnerability/modeling/new_vulnerability_model/result_new_normvuln_H37Rv_biotinRS_03_20_2023.txt",
# dir1 = "/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/",
# fill1="#262626",
# border1="#262626",
#
# strain2="H37Rv", exp2="biotinRR", date2="03_20_2023",
# data2="/store/home/mad/vulnerability/modeling/new_vulnerability_model/result_new_normvuln_H37Rv_biotinRR_03_20_2023.txt",
# dir2="/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/",
# fill2="#008B8B",
# border2="#609393",
#
# cores=30,
# plot_dir="/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/comparisons/H37Rv_biotinRR_vs_H37Rv_biotinRS/plots")
#
# } else {
# opt = list(strain1="Smeg", exp1="ref", date1="03_20_2023",
# data1="/store/home/mad/vulnerability/modeling/new_vulnerability_model/result_new_normvuln_Smeg_ref_03_20_2023.txt",
# dir1 = "/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/",
# fill1="#262626",
# border1="#262626",
#
# strain2="Smeg", exp2="RR1", date2="03_20_2023",
# data2="/store/home/mad/vulnerability/modeling/new_vulnerability_model/result_new_normvuln_Smeg_RR1_03_20_2023.txt",
# dir2="/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/",
# fill2="#008B8B",
# border2="#609393",
#
# cores=30,
# plot_dir="/store/home/mad/vulnerability/modeling/new_vulnerability_model/results_guide_lambda/comparisons/Smeg_RR1_vs_Smeg_ref/plots")
#
# }
#
# opt = list(strain1="H37Rv", exp1="biotinRS", date1="06_10_2023",
# data1="/store/home/mad/vulnerability/results/H37Rv/biotinRS/06_10_2023/data_logfc_atc_H37Rv_biotinRS_06_10_2023.txt",
# dir1 = "/store/home/mad/vulnerability/results/H37Rv/biotinRS/06_10_2023/modeling/vulnerability/",
# label1="biotinRS",
#
# strain2="H37Rv", exp2="biotinRR", date2="06_10_2023",
# data2="/store/home/mad/vulnerability/results/H37Rv/biotinRR/06_10_2023/data_logfc_atc_H37Rv_biotinRR_06_10_2023.txt",
# dir2="/store/home/mad/vulnerability/results/H37Rv/biotinRR/06_10_2023/modeling/vulnerability/",
# label2="biotinRR",
#
# cores=30,
# plot_dir="/store/home/mad/vulnerability/results/testing/plots/Smeg_RR1_vs_Smeg_ref/")
if(opt$safe){
message("Being safe, will ignore plots that already exist.")
}
desired_strain1 = opt$strain1
label1 = paste(opt$strain1, opt$exp1, opt$date1, sep="_")
desired_strain2 = opt$strain2
label2 = paste(opt$strain2, opt$exp2, opt$date2, sep="_")
if (!is.null(opt$genes)){
desired_gene_path = opt$genes
} else {
desired_gene_path = ""
}
if (file.exists(opt$data1)){
DATA_PATH1 = opt$data1
} else {
DATA_PATH1 = file.path(opt$dir, paste0("data_", label1, ".txt"))
}
if (file.exists(opt$data2)){
DATA_PATH2 = opt$data2
} else {
DATA_PATH2 = file.path(opt$dir, paste0("data_", label2, ".txt"))
}
read_gene_data = function(path){
XFULL = read.table(path, sep="\t", stringsAsFactors = FALSE, header=T)
if (!("GENE" %in% colnames(XFULL))){gene_col = "ORF"
} else {gene_col = "GENE"}
clean_df = data.frame(list(GENE=unique(XFULL[[gene_col]])))
clean_df["ORFID"] = get_orf_id_from_gene_list(clean_df$GENE)
clean_df["NAME"] = get_name_from_gene_list(clean_df$GENE)
# ii_bad = is.na(XFULL$ESS)
# XFULL$ESS[ii_bad] = "N/A"
# XFULL[["ORF"]] = paste0(XFULL$gene, ":", XFULL$name)
return(clean_df)
}
message(sprintf("Reading %s data...\n", label1))
message(sprintf("\t file = %s...", DATA_PATH1))
data1 = read_gene_data(DATA_PATH1)
message(sprintf("Reading %s data...", label2))
message(sprintf("\t file = %s...", DATA_PATH2))
data2 = read_gene_data(DATA_PATH2)
if (file.exists(desired_gene_path)){
message("Taking set of genes from file: ", desired_gene_path)
raw_unique_genes = scan(desired_gene_path, what="character")
} else if (!is.null(opt$genes) & opt$genes != "") {
message("Taking set of genes from argument: ", opt$genes)
raw_unique_genes = unlist(strsplit(opt$genes, ","))
} else {
message("Taking set of genes from data")
raw_unique_genes = unique(c(unique(data1$ORF), unique(data2$ORF)))
}
unique_genes = get_clean_gene_list(raw_unique_genes, data1)
N = length(unique_genes)
message(sprintf("Plotting comparison plots on all %s genes...", N))
# run_model("MSMEG4621:proB", data, desired_strain, folder=label)
# output_prefix = file.path(opt$plot_dir, "plots/comparisons", paste(label2, "vs", label1, sep="_"))
output_prefix = opt$plot_dir
desired_gene_comparisons = list()
for(i in 1:N){
message(unique_genes[i])
gene = unique_genes[i]
name = strsplit(gene, ":")[[1]][2]
desired_gene_comparisons[[i]] = list(
list(strain=opt$strain1, exp=opt$exp1, gene=gene, name=name, label=paste0(name, " - ", opt$label1), dir=opt$dir1,
# fit_samples=fit_samples_A, model_data=model_data_A,
# Plot stuff
summary_color=opt$summary_color1, summary_alpha=opt$summary_alpha1, summary_size=opt$summary_size1,
band_color=opt$band_color1, band_alpha=opt$band_alpha1, band_size=opt$band_size1,
dot_color=opt$dot_color1, dot_alpha=opt$dot_alpha1, band_size=opt$dot_size1,
## Histograms
hist_color=opt$hist_color1, hist_size=opt$hist_size1, hist_alpha=opt$hist_alpha1,
border_color=opt$border_color1, border_size=opt$border_size1, border_alpha=opt$border_alpha1
),
list(strain=opt$strain2, exp=opt$exp2, gene=gene, name=name, label=paste0(name, " - ", opt$label2), dir=opt$dir2,
# fit_samples=fit_samples_A, model_data=model_data_A,
# Plot stuff
summary_color=opt$summary_color2, summary_alpha=opt$summary_alpha2, summary_size=opt$summary_size2,
band_color=opt$band_color2, band_alpha=opt$band_alpha2, band_size=opt$band_size2,
dot_color=opt$dot_color2, dot_alpha=opt$dot_alpha2, band_size=opt$dot_size2,
## Histograms
hist_color=opt$hist_color2, hist_size=opt$hist_size2, hist_alpha=opt$hist_alpha2,
border_color=opt$border_color2, border_size=opt$border_size2, border_alpha=opt$border_alpha2
)
)
}
#plot_comparisons_parallel_helper(desired_gene_comparisons[[1]], width=13)
error_results = mclapply(desired_gene_comparisons, plot_comparisons_parallel_helper, mc.cores=opt$cores,
width=opt$width, height=opt$height,
samples=1000, str_resolution = 0.01,
include_gamma=!opt$hide_gamma, include_legend=!opt$hide_legend,
target="beta_e",
y_min=NULL, y_max=NULL,
breaks=NULL, mc.preschedule=TRUE, format=opt$format, dot_style=opt$dot_style, safe=opt$safe)
message("Encountered errors for the following genes: ")
for (i in 1:length(error_genes)){
if(error_results[i]){
message(desired_gene_comparisons[[i]][1]$gene)
}
}