Last updated: 2021-04-20
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Knit directory: methyl-geneset-testing/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 72f9d4c | JovMaksimovic | 2021-04-19 | Fixed issues with supp fig 3 and 15. |
| html | 4c57176 | JovMaksimovic | 2021-04-13 | Build site. |
| Rmd | 910609a | JovMaksimovic | 2021-04-13 | Fixed supp fig 3 |
| Rmd | 4b03471 | JovMaksimovic | 2021-04-13 | Updated code for generating figures |
| Rmd | 697c330 | JovMaksimovic | 2021-04-12 | Updated figure numbering and labels |
| Rmd | a64bf72 | Jovana Maksimovic | 2021-04-12 | Added panels to supp fig 3 |
| Rmd | 5e34ed3 | JovMaksimovic | 2021-04-12 | Figure updates |
| html | bbf77e1 | JovMaksimovic | 2020-08-21 | Build site. |
| Rmd | e3b14f4 | JovMaksimovic | 2020-08-21 | wflow_publish(c("analysis/01_exploreArrayBiasEPIC.Rmd", "analysis/02_exploreArrayBias450.Rmd", |
| html | e66c39a | JovMaksimovic | 2020-08-14 | Build site. |
| Rmd | ad9e7be | JovMaksimovic | 2020-08-14 | wflow_publish(c("analysis/figures.Rmd", "analysis/gettingStarted.Rmd", |
| html | 555069b | JovMaksimovic | 2020-08-14 | Build site. |
| Rmd | 91699a8 | JovMaksimovic | 2020-08-14 | wflow_publish("analysis/_site.yml", republish = TRUE, all = TRUE) |
| Rmd | 2be6153 | JovMaksimovic | 2020-07-14 | Updated code for generating manuscript figures. |
| Rmd | cfcac1b | Jovana Maksimovic | 2020-07-09 | Updated paper figures. |
library(here)here() starts at /Users/maksimovicjovana/Work/Research/methyl-geneset-testinglibrary(patchwork)
library(ggplot2)
library(limma)
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──✓ tibble 3.1.0 ✓ dplyr 1.0.5
✓ tidyr 1.1.3 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.1
✓ purrr 0.3.4 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()library(ggplotify)
library(UpSetR)
source(here("code/utility.R"))
options(scipen=10000)The code in this document produces all of the panel figures in our manuscript and saves them as PDF files in the output/figures directory.
a <- readRDS(here("output/figures/Fig-1A.rds"))
b <- readRDS(here("output/figures/Fig-1B.rds"))
c <- readRDS(here("output/figures/Fig-1C.rds"))
d <- readRDS(here("output/figures/Fig-1D.rds"))
layout <- "
AAAABB
CCDDDD
"
cairo_pdf(here("output/figures/Fig-1.pdf"), width = 9)
a + b+ c + theme(legend.position = "bottom") +
wrap_elements(panel = d, clip = FALSE) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))`geom_smooth()` using method = 'loess' and formula 'y ~ x'dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/Fig-3A.rds"))
b <- readRDS(here("output/figures/Fig-3B.rds"))
c <- readRDS(here("output/figures/Fig-3C.rds"))
d <- readRDS(here("output/figures/Fig-3D.rds"))
layout <- "
AABBBB
CCDDDD
"
b$layers[[4]]$aes_params$size <- 2.1
cairo_pdf(here("output/figures/Fig-3.pdf"), width = 9)
a + theme(legend.position = "none") +
b + theme(legend.position = "top",
legend.key.size = unit(1, "lines")) +
c + theme(legend.position = "bottom",
legend.key.size = unit(1, "lines")) +
d + theme(legend.position = "bottom",
legend.text = element_text(size = 8),
legend.key.size = unit(1, "lines"),
axis.title.y = element_text(size = 9.5)) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/Fig-4A.rds"))
b <- readRDS(here("output/figures/Fig-4B.rds"))
c <- readRDS(here("output/figures/Fig-4C.rds"))
d <- readRDS(here("output/figures/Fig-4D.rds"))
layout <- "
AACCCC
AACCCC
BBCCCC
BBCCCC
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
"
cairo_pdf(here("output/figures/Fig-4.pdf"), width = 8, height = 12)
a + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
legend.box.just = 0,
axis.title = element_text(size = 8),
plot.margin = margin(0,0,0,0)) +
b + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
legend.box.just = 0,
axis.title.y = element_text(size = 7),
axis.text = element_text(size = 7),
plot.margin = margin(0,0,0,0)) +
c + guides(colour = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 9)) +
labs(y = "Prop. top 100 terms in truth set") +
wrap_elements(d) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/Fig-5A.rds"))
b <- readRDS(here("output/figures/Fig-5B.rds"))
c <- readRDS(here("output/figures/Fig-5C.rds"))
d <- readRDS(here("output/figures/Fig-5D.rds"))
e <- readRDS(here("output/figures/Fig-5E.rds"))
f <- readRDS(here("output/figures/Fig-5F.rds"))
g <- readRDS(here("output/figures/Fig-5G.rds"))
layout <- "
AAACCCCC
AAACCCCC
BBBCCCCC
BBBCCCCC
DDDDDDDD
DDDDDDDD
DDDDDDDD
DDDDDDDD
DDDDDDDD
DDDDDDDD
EEEFFGGG
EEEFFGGG
EEEFFGGG
EEEFFGGG
EEEFFGGG
EEEFFGGG
"
cairo_pdf(here("output/figures/Fig-5.pdf"), width = 9, height = 10)
a + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
axis.title = element_text(size = 9),
axis.text = element_text(size = 8),
text = element_text(family = "arial")) +
b + guides(fill = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 8),
text = element_text(family = "arial")) +
c + theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
plot.title = element_blank(),
axis.title = element_text(size = 8),
text = element_text(family = "arial")) +
wrap_elements(d + theme(plot.title = element_blank(),
legend.box = "horizontal",
legend.text = element_text(size = 7),
legend.key.size = unit(1, "lines"),
legend.title = element_text(size = 8),
axis.text.y = element_text(size = 7),
text = element_text(family = "arial"))) +
wrap_elements(panel = e, clip = FALSE) +
wrap_elements(panel = f + theme(axis.title = element_text(size = 9)),
clip = FALSE) +
wrap_elements(panel = g, clip = FALSE) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))`geom_smooth()` using method = 'loess' and formula 'y ~ x'dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-1A.rds"))
b <- readRDS(here("output/figures/SFig-1B.rds"))
layout <- "
AAA
BBB
"
cairo_pdf(here("output/figures/SFig-01.pdf"))
a + wrap_elements(b) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-3A.rds"))
b <- readRDS(here("output/figures/SFig-3B.rds"))
c <- readRDS(here("output/figures/SFig-3C.rds"))
d <- readRDS(here("output/figures/SFig-3D.rds"))
e <- readRDS(here("output/figures/SFig-3E.rds"))
layout <- "
AABBBB
CCDDDD
EEEEEE
EEEEEE
EEEEEE
"
d$layers[[2]]$aes_params$size <- 0.2
a$layers[[1]]$aes_params$size <- 0.25
b$layers[[4]]$aes_params$size <- 2.1
cairo_pdf(here("output/figures/SFig-03.pdf"), width = 9, height = 13)
a + theme(legend.position = "none",
axis.title = element_text(size = 9)) +
b + theme(axis.title.x = element_text(size = 9),
axis.title.y = element_text(size = 8),
legend.position = "top",
legend.text = element_text(size = 8),
legend.title = element_text(size = 9)) +
c + theme(axis.title = element_text(size = 9),
legend.position = "bottom",
legend.text = element_text(size = 8),
legend.title = element_text(size = 9)) +
d + theme(axis.title.x = element_text(size = 9),
axis.title.y = element_text(size = 8),
legend.position = "bottom",
legend.text = element_text(size = 7),
legend.title = element_text(size = 9, angle = 90)) +
wrap_elements(e) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-4A.rds"))
b <- readRDS(here("output/figures/SFig-4B.rds"))
c <- readRDS(here("output/figures/SFig-4C.rds"))
d <- readRDS(here("output/figures/SFig-4D.rds"))
e <- readRDS(here("output/figures/SFig-4E.rds"))
f <- readRDS(here("output/figures/SFig-4F.rds"))
g <- readRDS(here("output/figures/SFig-4G.rds"))
layout <- "
AAABBB
CCCDDD
EEEEEE
FFFGGG
"
cairo_pdf(here("output/figures/SFig-04.pdf"), width = 8, height = 10)
a + scale_y_continuous(labels = scales::scientific) +
theme(legend.position = "right",
legend.box = "vertical",
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
axis.title = element_text(size = 9),
axis.text.x = element_text(size = 5)) +
b + theme(legend.box = "vertical",
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
axis.title = element_text(size = 9),
axis.text.x = element_text(size = 5)) +
c + theme(legend.text = element_text(size = 7),
legend.title = element_text(size = 8)) +
d + theme(legend.text = element_text(size = 8),
legend.title = element_text(size = 8),
axis.title = element_text(size = 8),
axis.text = element_text(size = 7),
legend.position = "bottom") +
e + theme(legend.position = "bottom") +
f +
g + theme(legend.text = element_text(size = 8),
legend.title = element_text(size = 8),
axis.title = element_text(size = 8),
legend.position = "right") +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-5A.rds"))
b <- readRDS(here("output/figures/SFig-5B.rds"))
layout <- "
AAAA
BBBB
BBBB
BBBB
"
cairo_pdf(here("output/figures/SFig-05.pdf"), width = 8, height = 9)
wrap_elements(a + theme(plot.title = element_blank(),
axis.title = element_text(size = 9),
legend.position = "right") +
labs(y = "Prop. top 100 terms in truth set")) +
wrap_elements(b) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-6A.rds"))
b <- readRDS(here("output/figures/SFig-6B.rds"))
layout <- "
AAAA
BBBB
BBBB
BBBB
"
cairo_pdf(here("output/figures/SFig-06.pdf"), width = 8, height = 9)
wrap_elements(a + theme(plot.title = element_blank(),
axis.title = element_text(size = 9),
legend.position = "right") +
labs(y = "Prop. top 100 terms in truth set")) +
wrap_elements(b) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-7A.rds"))
b <- readRDS(here("output/figures/SFig-7B.rds"))
c <- readRDS(here("output/figures/SFig-7C.rds"))
d <- readRDS(here("output/figures/SFig-7D.rds"))
e <- readRDS(here("output/figures/SFig-7E.rds"))
layout <- "
AAAA
AAAA
BBBB
BBBB
CCCC
CCCC
CCCC
CCCC
DDDD
DDDD
DDDD
DDDD
EEEE
EEEE
EEEE
EEEE
"
cairo_pdf(here("output/figures/SFig-07.pdf"), width = 8, height = 22)
wrap_elements((a + plot_layout(guides = "collect") &
theme(legend.box = "vertical",
legend.position = "right"))) +
wrap_elements((b + plot_layout(guides = "collect") &
theme(legend.box = "vertical",
legend.position = "right"))) +
c +
d +
e +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 f8a <- readRDS(here("output/figures/SFig-8A.rds"))
f8b <- readRDS(here("output/figures/SFig-8B.rds"))
f8c <- readRDS(here("output/figures/SFig-8C.rds"))
f8d <- readRDS(here("output/figures/SFig-8D.rds"))
layout <- "
AACCCC
AACCCC
BBCCCC
BBCCCC
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
DDDDDD
"
cairo_pdf(here("output/figures/SFig-08.pdf"), width = 8, height = 12)
f8a + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
legend.box.just = 0,
axis.title = element_text(size = 8),
plot.margin = margin(0,0,0,0)) +
f8b + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 7),
legend.title = element_text(size = 8),
legend.box.just = 0,
axis.title.y = element_text(size = 7),
axis.text = element_text(size = 7),
plot.margin = margin(0,0,0,0)) +
f8c + guides(colour = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 9)) +
labs(y = "Prop. top 100 terms in truth set") +
wrap_elements(f8d) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-9A.rds"))
b <- readRDS(here("output/figures/SFig-9B.rds"))
layout <- "
AAAA
BBBB
BBBB
BBBB
"
cairo_pdf(here("output/figures/SFig-09.pdf"), width = 8, height = 9)
wrap_elements(a + theme(plot.title = element_blank(),
axis.title = element_text(size = 9),
legend.position = "right") +
labs(y = "Prop. top 100 terms in truth set")) +
wrap_elements(b) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-10A.rds"))
b <- readRDS(here("output/figures/SFig-10B.rds"))
c <- readRDS(here("output/figures/SFig-10C.rds"))
d <- readRDS(here("output/figures/SFig-10D.rds"))
e <- readRDS(here("output/figures/SFig-10E.rds"))
f <- readRDS(here("output/figures/SFig-10F.rds"))
layout <- "
AAABBBBB
CCCCCCCC
CCCCCCCC
DDDEEFFF
DDDEEFFF
"
cairo_pdf(here("output/figures/SFig-10.pdf"), width = 8, height = 9)
a + guides(fill = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 8)) +
labs(y = "Prop. top 100 terms in truth set") +
b + theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
plot.title = element_blank(),
axis.title = element_text(size = 8)) +
wrap_elements(c + theme(plot.title = element_blank(),
legend.box = "horizontal",
legend.text = element_text(size = 7),
legend.key.size = unit(1, "lines"),
legend.title = element_text(size = 8),
axis.text.y = element_text(size = 7))) +
wrap_elements(panel = d, clip = FALSE) +
wrap_elements(panel = e + theme(axis.title = element_text(size = 8)),
clip = FALSE) +
wrap_elements(panel = f, clip = FALSE) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))`geom_smooth()` using method = 'loess' and formula 'y ~ x'dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-11A.rds"))
b <- readRDS(here("output/figures/SFig-11B.rds"))
c <- readRDS(here("output/figures/SFig-11C.rds"))
d <- readRDS(here("output/figures/SFig-11D.rds"))
e <- readRDS(here("output/figures/SFig-11E.rds"))
f <- readRDS(here("output/figures/SFig-11F.rds"))
layout <- "
AAABBBBB
CCCCCCCC
CCCCCCCC
DDDEEFFF
DDDEEFFF
"
cairo_pdf(here("output/figures/SFig-11.pdf"), width = 8, height = 9)
a + guides(fill = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 8)) +
labs(y = "Prop. top 100 terms in truth set") +
b + theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
plot.title = element_blank(),
axis.title = element_text(size = 8)) +
wrap_elements(c + theme(plot.title = element_blank(),
legend.box = "horizontal",
legend.text = element_text(size = 7),
legend.key.size = unit(1, "lines"),
legend.title = element_text(size = 8),
axis.text.y = element_text(size = 7))) +
wrap_elements(panel = d, clip = FALSE) +
wrap_elements(panel = e + theme(axis.title = element_text(size = 8)),
clip = FALSE) +
wrap_elements(panel = f, clip = FALSE) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))`geom_smooth()` using method = 'loess' and formula 'y ~ x'dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-12A.rds"))
b <- readRDS(here("output/figures/SFig-12B.rds"))
c <- readRDS(here("output/figures/SFig-12C.rds"))
d <- readRDS(here("output/figures/SFig-12D.rds"))
e <- readRDS(here("output/figures/SFig-12E.rds"))
layout <- "
AAAA
BBBB
CCCC
CCCC
CCCC
CCCC
DDDD
DDDD
DDDD
DDDD
EEEE
EEEE
EEEE
EEEE
"
cairo_pdf(here("output/figures/SFig-12.pdf"), width = 8, height = 17)
a + theme(legend.position = "right",
axis.title.y = element_text(size = 8)) +
b + theme(legend.position = "none",
axis.title.y = element_text(size = 8)) +
c +
d +
e +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-13A.rds"))
b <- readRDS(here("output/figures/SFig-13B.rds"))
layout <- "
AAAA
BBBB
"
cairo_pdf(here("output/figures/SFig-13.pdf"), width = 9)
a + b +
plot_layout(design = layout, guides = "collect") +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-14A.rds"))
b <- readRDS(here("output/figures/SFig-14B.rds"))
c <- readRDS(here("output/figures/SFig-14C.rds"))
d <- readRDS(here("output/figures/SFig-14D.rds"))
e <- readRDS(here("output/figures/SFig-14E.rds"))
f <- readRDS(here("output/figures/SFig-14F.rds"))
layout <- "
AAABBBBB
CCCCCCCC
CCCCCCCC
DDDEEFFF
DDDEEFFF
"
cairo_pdf(here("output/figures/SFig-14.pdf"), width = 8, height = 9)
a + theme(legend.position = "bottom",
legend.key.size = unit(0.75, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
axis.title = element_text(size = 9),
axis.text = element_text(size = 8),
text = element_text(family = "arial")) +
b + guides(fill = guide_legend(ncol = 3)) +
theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
plot.title = element_blank(),
axis.title = element_text(size = 8),
text = element_text(family = "arial")) +
wrap_elements(c + theme(legend.position = "bottom",
legend.key.size = unit(1, "lines"),
legend.text = element_text(size = 8),
legend.title = element_text(size = 9),
legend.box.just = 0,
legend.box = "horizontal",
plot.title = element_blank(),
axis.title = element_text(size = 8),
text = element_text(family = "arial"))) +
wrap_elements(d + theme(plot.title = element_blank(),
legend.box = "horizontal",
legend.text = element_text(size = 7),
legend.key.size = unit(1, "lines"),
legend.title = element_text(size = 8),
axis.text.y = element_text(size = 7),
text = element_text(family = "arial"))) +
wrap_elements(panel = e + theme(axis.text = element_text(size = 7),
axis.title = element_text(size = 8)),
clip = FALSE) +
wrap_elements(panel = f + theme(axis.title = element_text(size = 9)),
clip = FALSE) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))`geom_smooth()` using method = 'loess' and formula 'y ~ x'dev.off()quartz_off_screen
2 a <- readRDS(here("output/figures/SFig-15A.rds"))
b <- readRDS(here("output/figures/SFig-15B.rds"))
c <- readRDS(here("output/figures/SFig-15C.rds"))
layout <- "
AAAA
BBBB
BBBB
CCCC
"
cairo_pdf(here("output/figures/SFig-15.pdf"), width = 8, height = 10)
wrap_elements(a + theme(legend.position = "right",
plot.title = element_blank())) +
wrap_elements(shift_legend(b + theme(
plot.title = element_blank()))) +
wrap_elements(c + theme(plot.title = element_blank())) +
plot_layout(design = layout) +
plot_annotation(tag_levels = 'A') &
theme(plot.tag = element_text(size = 14, face = "bold"))
dev.off()quartz_off_screen
2
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] UpSetR_1.4.0 ggplotify_0.0.5 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[9] tibble_3.1.0 tidyverse_1.3.0 limma_3.46.0 ggplot2_3.3.3
[13] patchwork_1.1.1 here_1.0.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-152 fs_1.5.0 lubridate_1.7.10
[4] RColorBrewer_1.1-2 httr_1.4.2 rprojroot_2.0.2
[7] tools_4.0.3 backports_1.2.1 bslib_0.2.4
[10] utf8_1.2.1 R6_2.5.0 DBI_1.1.1
[13] BiocGenerics_0.36.0 mgcv_1.8-34 colorspace_2.0-0
[16] withr_2.4.1 tidyselect_1.1.0 gridExtra_2.3
[19] compiler_4.0.3 git2r_0.28.0 cli_2.4.0
[22] rvest_1.0.0 xml2_1.3.2 labeling_0.4.2
[25] sass_0.3.1 scales_1.1.1 digest_0.6.27
[28] rmarkdown_2.7 pkgconfig_2.0.3 htmltools_0.5.1.1
[31] dbplyr_2.1.1 rlang_0.4.10 readxl_1.3.1
[34] rstudioapi_0.13 gridGraphics_0.5-1 jquerylib_0.1.3
[37] farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[40] magrittr_2.0.1 Matrix_1.3-2 Rcpp_1.0.6
[43] munsell_0.5.0 S4Vectors_0.28.1 fansi_0.4.2
[46] lifecycle_1.0.0 stringi_1.5.3 whisker_0.4
[49] yaml_2.2.1 plyr_1.8.6 grid_4.0.3
[52] parallel_4.0.3 promises_1.2.0.1 crayon_1.4.1
[55] lattice_0.20-41 cowplot_1.1.1 haven_2.3.1
[58] splines_4.0.3 hms_1.0.0 knitr_1.31
[61] pillar_1.5.1 stats4_4.0.3 reprex_2.0.0
[64] glue_1.4.2 evaluate_0.14 BiocManager_1.30.12
[67] modelr_0.1.8 vctrs_0.3.7 httpuv_1.5.5
[70] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[73] xfun_0.22 broom_0.7.6 later_1.1.0.1
[76] lemon_0.4.5 rvcheck_0.1.8 IRanges_2.24.1
[79] ellipsis_0.3.1