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figure1.R
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figure1.R
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# Analyze mutational signatures per individual (lots of PCAs)
# Set working directory here
# setwd("~/Documents/Harris_project_directory")
# Need to comment which figure panels
options(stringsAsFactors = F)
library(ggplot2)
library(ggridges)
library(plyr)
library(RSvgDevice)
library(ggfortify)
library(scales)
library(grid)
library(gridExtra)
library(cowplot)
source("./common.R")
ncnr_trinuc_composition <- read.table("./hg18_ncnr_3mer_content.txt", header = T)
early_rep_trinuc_composition <- read.table("./hg18_replication_timing_q3_3mer_content.txt", header = T)
late_rep_trinuc_composition <- read.table("./hg18_replication_timing_q0_3mer_content.txt", header = T)
ncnr_spectra <- load_indiv_3mer_spectrum("hg18_ncnr", nmer_dir = "./nmer_mutation_counts/")
early_rep_spectra <- load_indiv_3mer_spectrum("hg18_replication_timing_q3", nmer_dir = "./nmer_mutation_counts/")
late_rep_spectra <- load_indiv_3mer_spectrum("hg18_replication_timing_q0", nmer_dir = "./nmer_mutation_counts/")
ncnr_spectra_reweight <- reweight_indiv_spectra(ncnr_spectra, ncnr_trinuc_composition, ncnr_trinuc_composition)
early_rep_spectra_reweight <- reweight_indiv_spectra(early_rep_spectra, early_rep_trinuc_composition, ncnr_trinuc_composition)
late_rep_spectra_reweight <- reweight_indiv_spectra(late_rep_spectra, late_rep_trinuc_composition, ncnr_trinuc_composition)
indiv_df <-
data.frame(
"indiv" = rownames(ncnr_spectra_reweight),
"subspecies" = sub("-.*", "", rownames(ncnr_spectra_reweight))
)
indiv_df$species <-
sapply(indiv_df$subspecies,
function(x)
if(startsWith(x, "Gorilla")) "Gorilla" else
if(startsWith(x, "Pan_troglodytes")) "Pan_troglodytes" else x)
ncnr_pca <-
prcomp(
ncnr_spectra_reweight,
scale. = T
)
indiv_df_ncnr_rep_time <-
data.frame(
"indiv" =
c(rownames(ncnr_spectra_reweight),
rownames(early_rep_spectra_reweight),
rownames(late_rep_spectra_reweight)),
"subspecies"=
c(
sub("-.*", "", rownames(ncnr_spectra_reweight)),
sub("-.*", "", rownames(early_rep_spectra_reweight)),
sub("-.*", "", rownames(late_rep_spectra_reweight))
),
"spectrum" = c(rep("ncnr", nrow(ncnr_spectra_reweight)),
rep("early_rep", nrow(early_rep_spectra_reweight)),
rep("late_rep", nrow(late_rep_spectra_reweight)))
)
indiv_df_ncnr_rep_time$species <-
sapply(indiv_df_ncnr_rep_time$subspecies,
function(x)
if(startsWith(x, "Gorilla")) "Gorilla" else
if(startsWith(x, "Pan_troglodytes")) "Pan_troglodytes" else x)
ncnr_early_late_rep_pca <-
prcomp(
rbind(
ncnr_spectra_reweight,
early_rep_spectra_reweight,
late_rep_spectra_reweight
),
scale. = T
)
spectra_by_species_replication_timing <-
lapply(
species,
function(s)
rbind(
subset(ncnr_spectra_reweight, startsWith(rownames(ncnr_spectra_reweight), s)),
subset(early_rep_spectra_reweight, startsWith(rownames(ncnr_spectra_reweight), s)),
subset(late_rep_spectra_reweight, startsWith(rownames(ncnr_spectra_reweight), s))
)
)
names(spectra_by_species_replication_timing) <- species
ncnr_early_late_rep_pca_by_species <-
lapply(
species,
function(s)
prcomp(
spectra_by_species_replication_timing[[s]],
scale. = T
)
)
names(ncnr_early_late_rep_pca_by_species) <- species
indiv_df_by_species_ncnr_early_late_rep <-
lapply(
species,
function(s){
n_indiv = nrow(subset(ncnr_spectra, startsWith(rownames(ncnr_spectra), s)))
return(
data.frame(
"indiv" = rownames(spectra_by_species_replication_timing[[s]]),
"subspecies" = sub("-.*", "", rownames(spectra_by_species_replication_timing[[s]])),
"spectrum" = c(rep("NCNR", n_indiv),
rep("early_rep", n_indiv),
rep("late_rep", n_indiv)
))
)
}
)
names(indiv_df_by_species_ncnr_early_late_rep) <- species
ggsave(
"./images/rep_timing_pca_Homo_pc1_pc2.pdf",
ggplot(
cbind(ncnr_early_late_rep_pca_by_species$Homo$x, indiv_df_by_species_ncnr_early_late_rep$Homo),
aes(x=PC1, y=PC2, group=subspecies)) +
geom_point(aes(shape=spectrum, color=subspecies, fill = subspecies), size=5) +
scale_shape_manual(values = c(17, 15, 16))+
scale_color_manual(values=subspecies_colors[4]) +
scale_fill_manual(values=subspecies_colors[4]) +
xlab(generate_pc_axis_label(ncnr_early_late_rep_pca_by_species$Homo, 1)) +
ylab(generate_pc_axis_label(ncnr_early_late_rep_pca_by_species$Homo, 2)),
width = 7, height = 4)
ggsave("./images/pca_ncnr_pc1_pc2.pdf",
ggplot(
cbind(ncnr_pca$x, indiv_df),
aes(x=PC1, y=PC2, group=subspecies)) +
geom_point(aes(fill=subspecies), colour="black", pch=21, size=5) +
scale_fill_manual(values=subspecies_colors) +
xlab(generate_pc_axis_label(ncnr_pca, 1)) +
ylab(generate_pc_axis_label(ncnr_pca, 2)),
width=7, height=4)
ggsave(
"./images/pca_ncnr_rep_timing_pc1_pc2.pdf",
ggplot(
cbind(ncnr_early_late_rep_pca$x, indiv_df_ncnr_rep_time),
aes(x=PC1, y=PC2, group=subspecies)) +
geom_point(aes(color=subspecies, shape=spectrum), size=5) +
scale_color_manual(values=subspecies_colors) +
xlab(generate_pc_axis_label(ncnr_early_late_rep_pca, 1)) +
ylab(generate_pc_axis_label(ncnr_early_late_rep_pca, 2)),
width = 7, height = 4)
ggsave("./images/ridgeplot_subset_ncnr.pdf",
plot_indiv_compartment_chisq(ncnr_spectra,
ncnr_trinuc_composition,
ncnr_spectra,
ncnr_trinuc_composition,
"NCNR Chi2 Distribution",
c("Homo", "Pan_troglodytes", "Gorilla"))
)
early_rep_species_spectra <-
load_species_3mer_spectrum("hg18_replication_timing_q3", nmer_dir = "./nmer_mutation_counts/")
late_rep_species_spectra <-
load_species_3mer_spectrum("hg18_replication_timing_q0", nmer_dir = "./nmer_mutation_counts/")
early_rep_species_spectra_reweight_ncnr <-
reweight_species_spectra(early_rep_species_spectra,
early_rep_trinuc_composition,
ncnr_trinuc_composition)
late_rep_species_spectra_reweight_ncnr <-
reweight_species_spectra(late_rep_species_spectra,
late_rep_trinuc_composition,
ncnr_trinuc_composition)
ggsave(
"./images/late_v_early_rep_heatmap_Homo.pdf",
generate_heatmap_plot_single_species(
late_rep_species_spectra_reweight_ncnr,
early_rep_species_spectra_reweight_ncnr,
"Homo"
)
)
ggsave(
"./images/all_species_late_v_early_rep_heatmap.pdf",
generate_heatmap_plot_multiple_species(late_rep_species_spectra_reweight_ncnr,
early_rep_species_spectra_reweight_ncnr)
)