R包：Pophelper 作堆积柱状图

Pophelper（V 2.3.0)堆积柱状图的R包

包详细地址：http://www.royfrancis.com/pophelper/articles/index.html

1安装

安装pophelper库。源代码可以从GitHub获得。R(>= 3.5.0)。
需要依赖包：

install.packages(c("devtools","ggplot2","gridExtra","gtable","label.switching","tidyr"),dependencies=T)
## 然后安装pophelper
install.packages('pophelper')

加载和检查包

# load library
library(pophelper)

# check version
packageDescription("pophelper", fields="Version")

2、主要功能

# convert q-matrix run files (structure, tess 2.3, baps, basic, clumpp) 
# to R qlist object
readQ() 
# convert TESS3 R list object to qlist object
readQTess3()
# collate/tabulate a qlist
tabulateQ() 
# summarise an output from tabulateQ()  
summariseQ()  
# Align clusters  
alignK()  
# create single-line barplots from qlist
plotQ()  
# create multi-line barplots from qlist
PlotQMultiline()  
# export files for DISTRUCT from qlist
distructExport()  
# Run and plot the Evanno method for STRUCTURE data
evannoMethodStructure()  
# collect TESS output from multiple directories into one
collectRunsTess()  

# wrapper function to tabulate, summarise, perform evanno method and generate barplots from filenames/paths.
analyseQ()             

3.输入文件

## 直接把需要用的文件全部替换到该R包测试文件中，省事儿
sfiles1 <- list.files(path=system.file("files/structure-ci",package="pophelper"),full.names=TRUE)
slist1 <- readQ(files=sfiles1, readci=TRUE)

## 需要准备一个标签文件，后面生成标签组，标签数据多就不必每个标签都显示，太乱，重叠起来了都。
## 我弄了1列标签名，与上面数据行数相同
threelabset <- read.delim(file = "D:/bioinformation/test/test/test/Results/structure_R/pophelper_learning/individual_lable.txt", header=T,stringsAsFactors=F)

4. 作图

plotQ(slist_test,imgoutput = "join", outputfilename="plotq4",imgtype="png", panelspacer =0.05, height = 0.5, splabangle = 0, showsp = FALSE,sppos = "left", splab = c("K=2", "K=3", "K=4","K=5","K=6", "K=7","K=8", "K=9"),showindlab = FALSE,grplab = onelabset1, grplabangle = 90,grplabsize = 0.82,grplabheight = 45)
## 这个包参数太多，根据需要慢慢查。。。

参数的用途如下图。标签名太多其实也不好处理，调整角度和字体大小如果都不合适，怕是只能ps了。