【原】不好好做圖的NSC系列(八):ggplot2重現(xiàn)Nature文章多組柱狀圖+散點(diǎn),，這是一場硬仗

TS的美夢 2022-01-22

展開全文

最近,，看到一篇nature文章,，整篇文章的圖的風(fēng)格類似于如下圖1,，因為第一次見這種圖,，感覺展示效果不錯,，所以嘗試做一下,！

Fluhr, L., Mor, U., Kolodziejczyk, A.A. et al. Gut microbiota modulates weight gain in mice after discontinued smoke exposure,，Nature，2021.

本來看著Figure1 h很簡單,，就先復(fù)現(xiàn)它了,，結(jié)果我錯了，它真的太麻煩了,，網(wǎng)上關(guān)于ggplot做多組柱狀圖深入修飾的教程也比較少,。直到最后，我也沒有完全復(fù)現(xiàn)它的樣子,。問題是：如何改變分組的填充,，但是點(diǎn)的顏色不變！

（我復(fù)現(xiàn)的圖,，有9分相似）

這篇Nature文章提供了作圖數(shù)據(jù),，在附件Source Data Fig. 1,，有Figure1作圖需要的所有數(shù)據(jù)。首先我們讀入數(shù)據(jù),，并通過因子設(shè)置變量順序與原文一致,！

setwd("F:/生物信息學(xué)/NATURE折線圖")A <- read.csv("A.csv",header = T)library(ggplot2)library(forcats)A$condictions <- as.factor(A$condictions)A$condictions <- fct_inorder(A$condictions)A$group <- as.factor(A$group)A$group <- fct_inorder(A$group)

接著就比較直接了，畫柱狀圖,。

ggplot(A, aes(fill=condictions, y=values, x=group))+  geom_bar(position=position_dodge(),stat="summary",colour = "black",size=1)+  theme_classic(base_size = 12)

這個柱狀圖就是普通的柱狀圖,，到這一步，我們需要思考下,，一步一步先解決這幾個問題,，柱狀圖坐落在坐標(biāo)上，柱子之間有空隙,，改變legend位置為水平,，設(shè)置x，y軸標(biāo)題,。

ggplot(A, aes(fill=condictions, y=values, x=group))+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  theme_classic(base_size = 12)+  theme(legend.direction = "horizontal", legend.position = "top")+  labs(title = "", y="Fecal calories per g", x = "")+  scale_y_continuous(limits = c(0,6000),expand = c(0,0))+  theme(axis.text.x = element_text(size = 12))+  theme(axis.text.y = element_text(size = 12))+  theme(axis.title = element_text(size = 14))

然后就是這幅圖比較特色的地方了,，添加分割線，右側(cè)有填充,，本來是一個簡單的事情,，但是由于橫坐標(biāo)不是數(shù)字，而是因子,，所以這里有點(diǎn)區(qū)別,。

ggplot(A, aes(fill=condictions, y=values, x=group))+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  theme_classic(base_size = 12)+  geom_vline(aes(xintercept=as.numeric(as.factor(group))+0.5),linetype=2,cex=1.2)+  geom_rect(aes(xmin=as.numeric(as.factor(group))+0.5,                xmax=Inf, ymin=(-Inf),ymax=Inf),            fill='grey90',color='grey90')+  geom_vline(xintercept =A$condictions,linetype=2,cex=1.2)+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  theme(legend.direction = "horizontal", legend.position = "top")+  labs(title = "", y="Fecal calories per g", x = "")+  scale_y_continuous(limits = c(0,6000),expand = c(0,0))+  theme(axis.text.x = element_text(size = 12))+  theme(axis.text.y = element_text(size = 12))+  theme(axis.title = element_text(size = 14))

圖的主體已經(jīng)出來了，接著添加誤差線,，我這里選擇了stat_summary函數(shù),，這個方法比較簡單，但是也有自己計算添加的,，比較麻煩,。這里需要注意的是添加誤差線的位置！

ggplot(A, aes(fill=condictions, y=values, x=group))+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  theme_classic(base_size = 12)+  geom_vline(aes(xintercept=as.numeric(as.factor(group))+0.5),linetype=2,cex=1.2)+  geom_rect(aes(xmin=as.numeric(as.factor(group))+0.5,                xmax=Inf, ymin=(-Inf),ymax=Inf),            fill='grey90',color='grey90')+  geom_vline(xintercept =A$condictions,linetype=2,cex=1.2)+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  stat_summary(fun.data = 'mean_se', geom = "errorbar", colour = "black",               width = 0.2,position = position_dodge(1))+  theme(legend.direction = "horizontal", legend.position = "top")+  labs(title = "", y="Fecal calories per g", x = "")+  scale_y_continuous(limits = c(0,6000),expand = c(0,0))+  theme(axis.text.x = element_text(size = 12))+  theme(axis.text.y = element_text(size = 12))+  theme(axis.title = element_text(size = 14))

最后就是比較難的內(nèi)容了,，包括添加散點(diǎn),，添加顯著性！到這里真的是做了一天了,，但是還是有一個問題沒有解決,，不能像原文那樣,，柱子為白色,，點(diǎn)為自己的顏色，不知道有沒有簡單的方法,！

ggplot(A, aes(fill=condictions, y=values, x=group))+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  theme_classic(base_size = 12)+  geom_vline(aes(xintercept=as.numeric(as.factor(group))+0.5),linetype=2,cex=1.2)+  geom_rect(aes(xmin=as.numeric(as.factor(group))+0.5,                xmax=Inf, ymin=(-Inf),ymax=Inf),            fill='grey90',color='grey90')+  geom_vline(xintercept =A$condictions,linetype=2,cex=1.2)+  geom_bar(position=position_dodge(1),stat="summary",width=0.7,colour = "black",size=1)+  stat_summary(fun.data = 'mean_se', geom = "errorbar", colour = "black",               width = 0.2,position = position_dodge(1))+  theme(legend.direction = "horizontal", legend.position = "top")+  labs(title = "", y="Fecal calories per g", x = "")+  scale_y_continuous(limits = c(0,6000),expand = c(0,0))+  theme(axis.text.x = element_text(size = 12))+  theme(axis.text.y = element_text(size = 12))+  theme(axis.title = element_text(size = 14))+  geom_jitter(data = A, aes(y = values),size = 3, shape = 21,              stroke = 0.01, show.legend = FALSE,               position = position_jitterdodge(jitter.height=1,dodge.width = 1))+  geom_signif(y_position=c(5000,5000,5000,5500), xmin=c(0.6,1.1,1.6,1.9), xmax=c(0.8,1.3,1.8,2.3),               annotation=c("**","**","****","****"), tip_length=0, size=0.8, textsize = 7,               vjust = 0.3)+  scale_fill_manual(values = c('#5494cc','#e18283','#0d898a','#f9cc52'))