shell散点图_两种方法批量绘制散点图

小技巧分享。

模拟数据

就模拟一个基因表达矩阵吧，列是基因，有10个基因，然后行是样本，这10个基因在100个样本的表达量。

expr=rnorm(1000)

dim(expr)=c(100,10)

colnames(expr)=LETTERS[1:10]

ITH_genes=LETTERS[1:10]

math=rbinom(10)

有一个变量是math值，也是100个样本的一个指标，然后就可以看10个基因分别和这个math的散点图，看相关性。

使用

这个时候表达矩阵是宽的

box

dat=data.frame(gene=as.numeric(expr[,i]),

math=math)

head(dat)

## 画boxplot

library(ggpubr)

ggscatter(dat, x = "gene", y = "math",

color = 'black', shape = 21, size = 0.5, # Points color, shape and size

add = "reg.line", # Add regressin line

add.params = list(color = "blue", fill = "lightgray"), # Customize reg. line

conf.int = TRUE, # Add confidence interval

cor.coef = TRUE, # Add correlation coefficient. see ?stat_cor

xlab = i,

cor.coeff.args = list(method = "pearson", label.sep = "\n")

)

})

library(cowplot)

plot_grid(plotlist=box, ncol=5 )

使用facet分面

这个时候宽表达矩阵，需要折叠起来，变成长的数据形式才能绘图。

library(reshape2)

dat=melt(expr)

dat[,1]=rep(math,100)

colnames(dat)=c('math','gene','value')

p=ggscatter(dat, y= "math", x = "value", shape = 21, size = 0.5,

add = "reg.line", # Add regressin line

add.params = list(color = "blue", fill = "lightgray"), # Customize reg. line

conf.int = TRUE, # Add confidence interval

cor.coef = TRUE, # Add correlation coefficient. see ?stat_cor

cor.coeff.args = list(method = "pearson" , label.sep = "\n")

)

facet(p, facet.by = "gene" )

全部代码

expr=rnorm(1000)

dim(expr)=c(100,10)

colnames(expr)=LETTERS[1:10]

ITH_genes=LETTERS[1:10]

math=rbinom(10)

box

dat=data.frame(gene=as.numeric(expr[,i]),

math=math)

head(dat)

## 画boxplot

library(ggpubr)

ggscatter(dat, x = "gene", y = "math",

color = 'black', shape = 21, size = 0.5, # Points color, shape and size

add = "reg.line", # Add regressin line

add.params = list(color = "blue", fill = "lightgray"), # Customize reg. line

conf.int = TRUE, # Add confidence interval

cor.coef = TRUE, # Add correlation coefficient. see ?stat_cor

xlab = i,

cor.coeff.args = list(method = "pearson", label.sep = "\n")

)

})

library(cowplot)

plot_grid(plotlist=box, ncol=5 )

library(reshape2)

dat=melt(expr)

dat[,1]=rep(math,100)

colnames(dat)=c('math','gene','value')

p=ggscatter(dat, y= "math", x = "value", shape = 21, size = 0.5,

add = "reg.line", # Add regressin line

add.params = list(color = "blue", fill = "lightgray"), # Customize reg. line

conf.int = TRUE, # Add confidence interval

cor.coef = TRUE, # Add correlation coefficient. see ?stat_cor

cor.coeff.args = list(method = "pearson" , label.sep = "\n")

)

facet(p, facet.by = "gene" )

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