数据分析笔记5气泡图绘制

应用案例：气泡图展示基因丰度

Fig.3.Relativenormalizedabundanceofmetabolicandfunctionalgenesinvolvedinenergygeneration,oxygentolerance,andbiogeochemicalcyclingfromBrothersvolcanometagenomeassemblies,includingthosediscussedinthetext.(A)BubblesrepresentsinglegenesorironmetabolismgenecategorieslistedinDatasetS2B.（Reysenbachetal.,;PNAS）

绘图代码

###bubbleplot

library(ggplot2)

library(reshape2)

pp-read.csv("D://RF_analysis.csv")#可后台获取

pp-pp[,1:8]

##构建数据框

io=melt(pp,id.vars=c("name"),value.name="Value",variable.name="Genes")####把宽数据变为长数据

head(io)

#io$sites=factor(io$sites,levels=unique(io$sites))####对样方排序

###转化数值型

io$Value-as.numeric(as.character(io$Value))

####转factor型

unique(io$name)

io$Phylum=factor(io$name)

####出图1

ggplot(io,aes(y=io$name,x=io$Genes))+

geom_point(aes(size=abs(Value),colour=Genes))+#,shape=1

scale_colour_manual(values=c("#B1A4C0","#E9B","#FDDC7B","#B2","#ACCDDC","#DD5F60","#F2B","#7CB6DB","pink2","skyblue","Gold2"))+

theme_bw(base_size=12)+

theme(axis.text.x=element_text(angle=45,hjust=1))+

#theme(legend.position="bottom",legend.direction="horizontal")+

#+labs(size="WindSpeed(mph)",fill="Months")#legendtitle

scale_size(range=c(0,9),breaks=c(0,10,20,40),limits=c(0,40))+

guides(colour=guide_legend(override.aes=list(size=5)))+

theme(axis.text=element_text(colour=black,size=9))

#####出图2

ggplot(io,aes(y=io$name,x=io$Genes))+

geom_point(aes(size=abs(Value),colour=Genes))+#,shape=1

scale_colour_manual(values=c("#B1A4C0","#E9B","#FDDC7B","#B2","#ACCDDC","#DD5F60","#F2B","#7CB6DB","pink2","skyblue","Gold2"))+

theme_bw(base_size=12)+

theme(axis.text.x=element_text(angle=45,hjust=1))+

#theme(legend.position="bottom",legend.direction="horizontal")+

#+labs(size="WindSpeed(mph)",fill="Months")#legendtitle

scale_size(range=c(0,9),breaks=c(0,10,20,40),limits=c(0,40))+

guides(colour=guide_legend(override.aes=list(size=5)))+

theme(axis.text=element_text(colour=black,size=9))+

theme(panel.background=element_rect(fill=white,colour=black),

panel.grid=element_blank(),

axis.title=element_text(color=black,size=9),

axis.ticks.length=unit(0.4,"lines"),axis.ticks=element_line(color=black),

axis.line=element_line(colour="black"),

axis.title.x=element_text(colour=black,size=9),

axis.title.y=element_text(colour=black,size=9),

axis.text=element_text(colour=black,size=9),

legend.title=element_blank(),

legend.text=element_text(size=9),

legend.key=element_blank(),

legend.background=element_rect(colour="white"))+

theme(axis.text.x=element_text(size=9,angle=45,hjust=1))