In shbrief/GenomicSuperSignaturePaper: Reproduce GenomicSuperSignature paper

knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, eval=FALSE)

suppressPackageStartupMessages({
  library(ggpubr)
})

Figure 3

a <- readRDS("outputs/scatter_834_833.rds")
b <- readRDS("outputs/boxplot_CMS_vs_834_833.rds")
c <- readRDS("outputs/boxplot_PCSS_vs_834_833.rds")

png("Figures/manuscript_Fig3a.png", res = 500, width = 5, height = 5, units = "in")
a
dev.off()
png("Figures/manuscript_Fig3b.png", res = 500, width = 5, height = 3, units = "in")
b
dev.off()
png("Figures/manuscript_Fig3c.png", res = 500, width = 5, height = 3, units = "in")
c
dev.off()

abc <- ggarrange(ggarrange(a$value, labels = "a"),
                 ggarrange(b$value, c$value,
                           labels = c("b", "c"),
                           nrow = 2, align = "hv",
                           heights = c(1, 1)),
                 ncol = 2,
                 widths = c(1.4, 1),
                 font.label = list(size = 15),
                 align = "hv")
abc

## Save Supplementary Figure 3
png("Figures/manuscript_Fig3.png", width = 1000, height = 550)
abc
dev.off()

## Clean-up
rm(a,b,c,abc)

Supplementary Figure 5

a <- readRDS("outputs/scatter_1575_834.rds")
b <- readRDS("outputs/boxplot_CMS_vs_1575_834.rds")
c <- readRDS("outputs/boxplot_PCSS_vs_1575_834.rds")
d <- readRDS("outputs/scatter_832_188.rds")
e <- readRDS("outputs/boxplot_CMS_vs_832_188.rds")
f <- readRDS("outputs/boxplot_PCSS_vs_832_188.rds")

all <- ggarrange(ggarrange(a$value, d$value,
                           labels = c("a", "d"), 
                           nrow = 2),
                 ggarrange(b$value, c$value, e$value, f$value,
                           labels = c("b", "c", "e", "f"),
                           nrow = 4),
                 ncol = 2,
                 widths = c(1.4, 1),
                 font.label = list(size = 15),
                 align = "hv")
all

## Save Supplementary Figure 3
png("Figures/manuscript_Sup_Fig5.png", width = 1000, height = 1100)
all
dev.off()

## Clean-up
rm(a,b,c,d,e,f,all)

Supplementary Figure 6

a <- readRDS("outputs/10_CRC_datasets/scatter_PCSS.rds")
b <- readRDS("outputs/10_CRC_datasets/scatter_834_833.rds")
c <- readRDS("outputs/10_CRC_datasets/boxplot_CMS_vs_PCSS.rds")
d <- readRDS("outputs/10_CRC_datasets/boxplot_CMS_vs_834_833.rds")
e <- readRDS("outputs/10_CRC_datasets/boxplot_PCSS_vs_834_833.rds")

all <- ggarrange(ggarrange(a, b$value,
                           labels = c("a", "b"), 
                           nrow = 2),
                 ggarrange(c$value, d$value, e$value,
                           labels = c("c", "d", "e"),
                           nrow = 3),
                 ncol = 2,
                 widths = c(1.4, 1),
                 font.label = list(size = 15),
                 align = "hv")
all

## Save Supplementary Figure 3
png("Figures/manuscript_Sup_Fig6.png", width = 700, height = 770)
all
dev.off()

## Clean-up
rm(a,b,c,d,e,all)