R命令实录

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读取dataframe的指定行或列

http://shichangshun.cn/2015/11/09/%E6%8A%80%E6%9C%AF/2015-11-09-Read-rows-col/

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if(!file.exists("read")){
  dir.create("read")
}# 创建工作路径文件夹
setwd("./read") # 设置工作路径
if(!file.exists("data")){
  dir.create("data")
} # 新建data文件夹

命令的重复

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var.genes=Reduce(intersect, var.genes1)

快速计算cor

library(HiClimR)
fastCor

数据框替换值

method1: 使用封装函数
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currentid
newid
pbmc$ident<- plyr::mapvalues(pbmc$ident，from=currentid,to=newid)
##### method2: 使用gsub
anno$celltype <- anno$cluster_new
anno$celltype <- paste0("_",paste0(anno$celltype,'_'))
ma$cluster <- paste0("_",paste0(ma$cluster,"_"))
for (i in unique(ma$cluster)) {
  anno$celltype <- gsub(anno$celltype,pattern = i,replacement = ma$V2[i])
  print(i)
}
method3: 使用%>%

trimws

替换开头或结尾的空格、换行符、制表符、回车。

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trimws(gene,which=c("both"), whitespace="[ \t\r\n]")

scale

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library(scales)
rss_ct_scale<-apply(rss_ct, 1, rescale,to=c(-2,2))

ggplot 多个画板一个图

示例

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######################################  same mouse
library(gridExtra)
library(ggplot2)
plot_correlation <- function(i){
  name1 <- paste0('T',paste0(i,"human"))
  name2 <- paste0('T',paste0(i+1,"human"))
  p<-ggplot(ave_teratoma, aes(x=get(name1), y=get(name2))) +
    geom_point(alpha=1, size=1) +
    geom_smooth(method="lm") +
    theme_bw() +
    xlab(name1)+ylab(name2)+
    ggtitle(paste0("Mouse",i/2-3))+
    theme(text = element_text(size=10), legend.title=element_blank(),plot.title = element_text(hjust = 0.5))+
    stat_fit_glance(method = 'lm',
                    
                    method.args = list(formula = y ~ x),
                    
                    mapping = aes(label = sprintf('R^2~"="~%.3f~~italic(P)~"="~%.2g', stat(r.squared), stat(p.value))),
                    
                    parse = TRUE,label.x = 0.95,label.y = 0.95)
}

plot_list <- lapply(seq(8,18,2), plot_correlation)
n <- length(plot_list)
nCol <- floor(sqrt(n))
grid.arrange(grobs = plot_list, ncol = nCol) ## display plot
ggsave(file = "same_mouse_correlation.png", arrangeGrob(grobs = plot_list, ncol = 2),height = 9,width = 6)  ## save plot