不積跬步，無(wú)以至千里
本期我們嘗試復(fù)現(xiàn)2023年3月7日發(fā)表在Nature Communications上的Non-canonical functions of SNAIL drive context-specific cancer progression文章中的Fig3a。
以下是原圖：
數(shù)據(jù)可以自行下載，也可評(píng)論區(qū)留言我私發(fā)給你。
代碼
- 讀入數(shù)據(jù)：
library(readr)
library(tidyr)
library(dplyr)
library(forcats)
library(magrittr)
library(ggplot2)
library(RColorBrewer)
library(ggtext)
data <- read_csv('Fig3a.csv')
head(data)
# A tibble: 3 × 6
# No. `Grade 1` `Grade 2` `Grade 3` `Grade 4` Total
# <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 PKrasG12D/+ 5 13 6 8 32
#2 PKrasG12D/+;SnailKI/+ 0 6 9 4 19
#3 PKrasG12D/+;SnailKI/KI 1 5 11 0 17
- 繪圖：
data %>%
pivot_longer(starts_with('Grade'), names_to = 'Class') %>%
mutate(Class = fct_relevel(Class, paste('Grade', rev(1:4), sep = " "))) %>%
ggplot(aes(x = No., y = value/Total)) +
geom_bar(aes(fill = Class),
position = 'stack',
stat = 'identity',
color = 'black',
width = 0.7,
linewidth = 0.5) +
scale_fill_manual(values = c('#084594', '#4292c6', '#9ecae1', '#deebf7')) +
scale_y_continuous(expand = c(0, 0),
breaks = seq(0, 1, 0.2),
labels = seq(0, 100, 20)) +
scale_x_discrete(labels = c('*PKras^G12D/+*',
'*PKras^G12D/+*;*Snail^KI/+*',
'*PKras^G12D/+*;*Snail^KI/KI*')) +
labs(x = '', y = 'Tumours (%)', title = 'PDAC') +
theme_classic() +
theme(plot.title = element_text(hjust = 0.5, family = 'sans', size = 13, color = 'black'),
legend.title = element_blank(),
axis.text.x = element_markdown(vjust = 1, hjust = 1, angle = 45),
axis.text = element_text(family = 'sans', color = 'black', size = 12),
axis.title = element_text(family = 'sans', color = 'black', size = 12),
axis.ticks.length.x = unit(0, units = 'cm'),
axis.ticks.y = element_line(colour = 'black'),
axis.line = element_line(colour = 'black'))
ggsave(filename = 'Fig3a.jpeg', width = 3, height = 3.5, dpi = 5000)
最終效果
寫在最后
這個(gè)圖里面有幾個(gè)我覺(jué)得是值得我們大家一起學(xué)習(xí)的：
使用
forcasts包靈活調(diào)整順序，比傳統(tǒng)的因子設(shè)置更方便；使用
ggtext包中的element_markdown()解讀markdown語(yǔ)法，讓我們可以書寫基因角標(biāo)。
