R语言可视化（十三）（气泡图绘制） R语言可视化（十三）：气泡图

13. 富集气泡图绘制清除当前环境中的变量

rm(list=ls())

设置工作目录

setwd("C:/Users/Dell/Desktop/R_Plots/13bubble/")

读取示例数据

data <- read.table("demo_bubble.tsv",header = T, check.names = F,sep="\t") head(data) Pathway R0vsR3 All_UnigenePvalueQvalue 1 Plant hormone signal transduction70254 3.94000e-09 4.33e-07 2Phenylpropanoid biosynthesis49163 5.07000e-08 2.79e-06 3Phenylalanine metabolism38126 1.53000e-06 4.20e-05 4Plant-pathogen interaction45159 1.21000e-06 4.20e-05 5Flavonoid biosynthesis1122 5.86000e-05 1.29e-03 6Linoleic acid metabolism1124 1.58824e-04 2.50e-03 richFactor Pathway ID 10.2755906ko04075 20.3006135ko00940 30.3015873ko00360 40.2830189ko04626 50.5000000ko00941 60.4583333ko00591

基础symbols函数绘制气泡图

head(mtcars) mpg cyl disphp dratwtqsec vs am gear carb Mazda RX421.06160 110 3.90 2.620 16.460144 Mazda RX4 Wag21.06160 110 3.90 2.875 17.020144 Datsun 71022.8410893 3.85 2.320 18.611141 Hornet 4 Drive21.46258 110 3.08 3.215 19.441031 Hornet Sportabout 18.78360 175 3.15 3.440 17.020032 Valiant18.16225 105 2.76 3.460 20.221031attach(mtcars) symbols(wt,mpg,circles=cyl, inches=0.2, bg=rainbow(7))

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# 添加文本标签 text(wt,mpg,labels = row.names(mtcars),cex=0.7,pos = 3,offset = 0.8)

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# 将圆圈换成正方形 symbols(wt,mpg,squares=cyl, inches=0.3, bg=rainbow(7)) detach(mtcars)

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image.png ggplot2包绘制富集气泡图

library(ggplot2) head(data) Pathway R0vsR3 All_UnigenePvalueQvalue 1 Plant hormone signal transduction70254 3.94000e-09 4.33e-07 2Phenylpropanoid biosynthesis49163 5.07000e-08 2.79e-06 3Phenylalanine metabolism38126 1.53000e-06 4.20e-05 4Plant-pathogen interaction45159 1.21000e-06 4.20e-05 5Flavonoid biosynthesis1122 5.86000e-05 1.29e-03 6Linoleic acid metabolism1124 1.58824e-04 2.50e-03 richFactor Pathway ID 10.2755906ko04075 20.3006135ko00940 30.3015873ko00360 40.2830189ko04626 50.5000000ko00941 60.4583333ko00591# 基础富集气泡图 ggplot(data,aes(x=richFactor,y=Pathway,size=R0vsR3,color=-log10(Qvalue))) + geom_point()

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# 更改颜色，主题，坐标轴标题 ggplot(data,aes(x=richFactor,y=Pathway,size=R0vsR3,color=-log10(Qvalue))) + geom_point() + theme_bw() + scale_colour_gradient(low="green",high="red") + labs(x="GeneRatio",y="Pathway",title="Top20 enriched pathways", colour=expression(-log[10]("QValue")),size="Gene number") + theme(plot.title = element_text(hjust = 0.5))

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image.png ggpubr包绘制富集气泡图

library(ggpubr) data$`-log10(Qvalue)` <- -log10(data$Qvalue)# 基础富集气泡图 ggscatter(data,x="richFactor",y="Pathway", size = "R0vsR3",color = "-log10(Qvalue)")

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# 更改颜色，主题，坐标轴标题 ggscatter(data,x="richFactor",y="Pathway", size = "R0vsR3",color = "-log10(Qvalue)", xlab="GeneRatio",ylab="Pathway", title="Top20 enriched pathways") + theme_minimal() + scale_colour_gradient(low="green",high="red") + labs(colour=expression(-log[10]("QValue")),size="Gene number") + theme(plot.title = element_text(hjust = 0.5),legend.position = "right")

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sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)Matrix products: defaultlocale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936 [3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_China.936attached base packages: [1] statsgraphicsgrDevices utilsdatasetsmethodsbaseother attached packages: [1] ggpubr_0.2.1magrittr_1.5ggplot2_3.2.0loaded via a namespace (and not attached): [1] Rcpp_1.0.5rstudioapi_0.10knitr_1.23tidyselect_0.2.5 [5] munsell_0.5.0colorspace_1.4-1 R6_2.4.0rlang_0.4.7 [9] dplyr_0.8.3tools_3.6.0grid_3.6.0gtable_0.3.0 [13] xfun_0.8withr_2.1.2htmltools_0.3.6yaml_2.2.0 [17] lazyeval_0.2.2assertthat_0.2.1 digest_0.6.20tibble_2.1.3 [21] ggsignif_0.5.0crayon_1.3.4purrr_0.3.2evaluate_0.14 [25] glue_1.3.1rmarkdown_1.13labeling_0.3compiler_3.6.0 [29] pillar_1.4.2scales_1.0.0pkgconfig_2.0.2