今天是轉錄組培訓最后一天，剩下一點時間自由探索。朋友們來自山南海北，還是北京的最多。

一位老師聊起火山圖（Volcano plot | 別再問我這為什么是火山圖 （在線輕松繪制）），說見過傾斜45度的類似圖，可否演示怎么畫？想了下，可能是下面這種圖，繪起來看看。

檢查和安裝包

a = rownames(installed.packages()) if (!requireNamespace("BiocManager", quietly = TRUE))install.packages("BiocManager", repos = site)a = rownames(installed.packages())install_bioc <-c("egg","ggpubr","ggplot2")for (i in install_bioc) {if (!i %in% a)BiocManager::install(i, update = F) }if (!"ImageGP" %in% a){# devtools::install_github("Tong-Chen/ImageGP")devtools::install_git("https://gitee.com/ct5869/ImageGP.git") }library(ImageGP) library(ggplot2) library(ggpubr) library(egg)

讀入數據并標記差異基因

數據是基于DESeq2分析的差異基因數據。

file <- "data/ehbio.simplier.DESeq2.trt._vs_.untrt.results.txt"diffexpr <- sp_readTable(file, row.names=1)# 做一個log轉換 diffexpr$trt <- log2(diffexpr$trt+1) diffexpr$untrt <- log2(diffexpr$untrt+1)head(diffexpr)## trt untrt baseMean log2FoldChange pvalue padj ## ENSG00000152583 10.88130 6.354646 983.042 4.546 1.219e-91 2.149e-87 ## ENSG00000189221 12.09256 8.706410 2391.559 3.387 9.955e-61 8.779e-57 ## ENSG00000179094 10.40316 7.343044 757.249 3.065 2.435e-54 1.432e-50 ## ENSG00000116584 10.50370 11.567470 2242.427 -1.064 3.957e-49 1.745e-45 ## ENSG00000120129 12.55314 9.579082 3386.426 2.975 1.930e-48 6.807e-45 ## ENSG00000134686 12.04738 10.587715 2884.847 1.460 1.846e-45 5.427e-42

標記差異基因

diffexpr$level <- ifelse(diffexpr$padj<0.05, ifelse(diffexpr$log2FoldChange>=1, "trt up", ifelse(diffexpr$log2FoldChange<=-1, "untrt up", "NoSig")),"NoSig") head(diffexpr)## trt untrt baseMean log2FoldChange pvalue padj level ## ENSG00000152583 10.88130 6.354646 983.042 4.546 1.219e-91 2.149e-87 trt up ## ENSG00000189221 12.09256 8.706410 2391.559 3.387 9.955e-61 8.779e-57 trt up ## ENSG00000179094 10.40316 7.343044 757.249 3.065 2.435e-54 1.432e-50 trt up ## ENSG00000116584 10.50370 11.567470 2242.427 -1.064 3.957e-49 1.745e-45 untrt up ## ENSG00000120129 12.55314 9.579082 3386.426 2.975 1.930e-48 6.807e-45 trt up ## ENSG00000134686 12.04738 10.587715 2884.847 1.460 1.846e-45 5.427e-42 trt up

基于ImageGP繪圖

p <- sp_scatterplot(diffexpr, xvariable = "trt", yvariable = "untrt", color_variable = "level",color_variable_order = c("NoSig","trt up", "untrt up"),manual_color_vector = c("grey","firebrick","dodgerblue"),legend.position = c(0.8,0.3)) + coord_fixed(1) p

到這滿足需求了，又有老師說能不能加上數據分布展示？

拼上Marginal plot

xplot <- ggplot(diffexpr, aes(x=trt)) + geom_histogram(fill="firebrick") +theme_classic() + theme(axis.line.x=element_blank(), axis.ticks.x=element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.border = element_blank(),panel.background = element_blank(),legend.title = element_blank(),legend.position = c(0.75,0.85),#legend.title = element_text(size = 5), legend.text = element_text(size = 8),legend.key.size = unit(0.5, "lines"),legend.spacing = unit(0.3, "cm"),) + ylab("Density") xplot

yplot <- ggplot(diffexpr, aes(x=untrt)) + geom_histogram(fill="dodgerblue") +theme_classic() +theme(axis.line.y=element_blank(), axis.ticks.y=element_blank(), axis.text.y = element_blank(), axis.title.y=element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.border = element_blank(),panel.background = element_blank(),legend.title = element_blank(),legend.position = c(0.7,0.8),#legend.title = element_text(size = 5), legend.text = element_text(size = 8),legend.key.size = unit(0.5, "lines"),legend.spacing = unit(0.3, "cm"),) + ylab("Density") +rotate() yplot

合并起來

white <- ggplot() + theme_void()egg::ggarrange(xplot, white, p, yplot, widths=c(5,2),heights = c(2,5),padding=unit(0,"line"))

也可以用現成的工具

用ggpubr繪制

ggscatterhist(diffexpr, x="trt", y="untrt", color="level",palette=c("grey","firebrick","dodgerblue"), margin.plot="histogram" )

輸出數據用在線工具繪制

見次條

高顏值免費在線繪圖工具

http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MTI%3D%27

sp_writeTable(diffexpr, file="DE_gene_label.txt")

數據和代碼見?https://gitee.com/ct5869/shengxin-baodian/Plot

往期精品(點擊圖片直達文字對應教程)

機器學習

后臺回復“生信寶典福利第一波”或點擊閱讀原文獲取教程合集

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