查詢ggprism包使用時候發(fā)現(xiàn)官網(wǎng)給出的一示例圖比較常用，這里記錄學(xué)習(xí)一下戴卜。
image-20221208130405959
加載R包準(zhǔn)備數(shù)據(jù)
## 加載R包
sapply(c('dplyr',"ggplot2","ggprism",
"ggbeeswarm","rstatix"), require, character.only = TRUE)
## 準(zhǔn)備數(shù)據(jù)
data("wings")
head(wings)
## 整理數(shù)據(jù)
wings$measure <- wings$measure %>%
gsub("\\.", " ", .) %>%
tools::toTitleCase() %>%
factor(., levels = c("Wing Size", "Cell Size", "Cell Number"))
head(wings)
# A tibble: 6 × 4
sex genotype measure percent.change
<fct> <fct> <fct> <dbl>
1 male Tps1MIC/+ Wing Size -2.45
2 male Tps1MIC/+ Cell Size 6.33
3 male Tps1MIC/+ Cell Number -8.41
4 male Tps1MIC/+ Wing Size -1.14
5 male Tps1MIC/+ Cell Size -2.53
6 male Tps1MIC/+ Cell Number 1.26
## 基本繪圖
p <- ggplot(wings, aes(x = measure, y = percent.change))+
ggbeeswarm::geom_beeswarm(
aes(fill = genotype),
dodge.width = 0.9,
shape = 21,
cex = 3.5
)
p
## 分面
p <- p+facet_wrap(
~sex,
scales = 'free',
labeller = labeller(sex = c(male = "\u2642", female = "\u2640"))
)+
geom_hline(yintercept = 0, linetype = 2, linewidth = 0.3)
p
image-20221222145913758
注意兩個細節(jié)：
- tools::toTitleCase可以替換字符中每個單詞的首字母大寫咖祭，str_to_title函數(shù)也可類似這種效果
TotitleCase函數(shù)源碼如下：
ToTitleCase <- function(x) {
paste0(toupper(substr(x, 1, 1)), substr(x, 2, nchar(x)))
}
- facet_wrap中的labeller屬性對不同的因子類型設(shè)置不同的標(biāo)記充蓝，例子中\(zhòng)u2642就是使用了unicode字符標(biāo)記君躺，推薦個Unicode Character Table便于查詢
image-20221222150440938
添加均值
p <- p + stat_summary(
geom = "crossbar",
aes(fill = genotype),
fun = mean,
position = position_dodge(0.9),
colour = "red",
linewidth = 0.4, width = 0.7,
show.legend = FALSE
)
p
image-20221222150633975
計算顯著性P值
wings_pvals <- wings %>%
group_by(sex, measure) %>%
rstatix::t_test(
percent.change ~ genotype,
p.adjust.method = "BH",
var.equal = TRUE,
ref.group = "Tps1MIC/+"
) %>%
rstatix::add_x_position(x = "measure", dodge = 0.9) %>% # dodge must match points
mutate(label = c("***", "*", "P = 0.26", "***", "***", "P = 0.65"))
p <- p + add_pvalue(
wings_pvals, y = 10, xmin = "xmin", xmax = "xmax", tip.length = 0,
fontface = "italic", lineend = "round", bracket.size = 0.5
)
p
image-20221222150718356
- 這里主要利用rstatix包中的t_test函數(shù)批量計算P值犹撒，使用add_x_position自動計算P值的位置,信息 最后通過add_pvalue函數(shù)根據(jù)位置信息自動標(biāo)記于圖中横腿。
image-20221222151131661
設(shè)置主題及配色
## 添加主題元素
p <- p + theme_prism(
base_fontface = "plain",
base_line_size = 0.7,
base_family = "Arial") +
scale_x_discrete(guide = guide_prism_bracket(width = 0.15),
labels = scales::wrap_format(5))+
scale_y_continuous(
limits = c(-20, 12),
expand = c(0, 0),
breaks = seq(-20, 10, 5),
guide = "prism_offset") +
labs(y = "% change") +
theme(
legend.position = "bottom",
axis.title.x = element_blank(),
strip.text = element_text(size = 14),
legend.spacing.x = unit(0, "pt"),
legend.text = element_text(margin = margin(r = 20))
) +
guides(fill = guide_legend(override.aes = list(size = 3)))
p
## 改變顏色及圖例文本格式
p <- p + scale_fill_manual(
values = c("#026FEE", "#87FFFF"),
labels = c(expression("Tps"*1^italic("MIC")~"/ +"),
expression("Tps"*1^italic("MIC")))
)
p
## 添加文本注釋
p <- p + geom_text(
data = data.frame(
sex = factor("female", levels = c("male", "female")),
measure = "Cell Number",
percent.change = -18.5,
lab = "(n = 10)"
),
aes(label = lab)
)
p
image-20221222151215683
雖說是一個簡單的示例圖, 但其中有很多細節(jié)調(diào)整值得去學(xué)習(xí)颓屑，而且這種類型的圖論文中也是比較常用的。
