R语言生信笔记

Table of Content

• R向xlsx中输出多个sheets
• 差异表达基因画HeatMap
• 基因symbols和ENSEMBL等ID转化
• Work on layout

检查R包的下载次数：

For the DR.SC package:

Downloads each month (https://cranlogs.r-pkg.org/badges/DR.SC)

Downloads in last day (https://cranlogs.r-pkg.org/badges/last-day/DR.SC)

Grand total (https://cranlogs.r-pkg.org/badges/grand-total/DR.SC)

将R中的BLAS替换成OpenBLAS加快计算速度：

在64位windows下安装OpenBLAS的步骤如下： 从压缩文件OpenBLAS-v0.2.8-x86_64-Win.zip中解压libopenblas.dll到R目录下64目录中。将此目录中Rblas.dll文件名改成Rblas.dll.back作为备份。将libopenblas.dll文件名改成Rblas.dll。 下载网址：https://github.com/xianyi/OpenBLAS/releases

R向xlsx中输出多个sheets

直接稍微修改下面的code即可，方便快捷。注意输入sheet前数据务必先转化为data frame格式。

for(i in 1:9){
  dat <- matrix(rnorm(50*4), 50, 4)
  dat <- as.data.frame(dat)
  colnames(dat) <- c('t value',' Pr(>|t|)',' FDR',' avg_log2FC')
  # xlsx::write.xlsx(dat, file='DEGs.xlsx', sheetName = paste0('sheet', i), append = T)
}

快速选择前n个差异表达基因的信息并画HeatMap

 ## DEG analysis based on the annotated labels
  # install.packages('DR.SC')
  suppressPackageStartupMessages(library(DR.SC)  )

## Warning: package 'spatstat.geom' was built under R version 4.0.5

## Warning: package 'spatstat.data' was built under R version 4.0.4

  seu <- gendata_RNAExp(height=20, width=20,p=200, K=4)
  library(Seurat)

## Attaching SeuratObject

  # standard log-normalization
  seu <- NormalizeData(seu)
  seu <- ScaleData(seu)

## Centering and scaling data matrix

  Idents(seu) <- factor(seu$true_clusters)
  dat <- FindAllMarkers(seu)

## Calculating cluster 1

## Calculating cluster 2

## Calculating cluster 3

## Calculating cluster 4

  suppressPackageStartupMessages(library(dplyr) )

## Warning: package 'dplyr' was built under R version 4.0.5

  dat %>%
    group_by(cluster) %>%
    top_n(n = 10, wt = avg_log2FC) -> top10
  seus <- subset(seu, downsample = 300)
## HeatMap
library(ggplot2)
p <- DoHeatmap(seus, features = top10$gene, label = F) + 
  theme(legend.text = element_text(size=16),
        legend.title = element_text(size=18, face='bold'),
        axis.text.y = element_text(size=14)) +
  guides(shape = guide_legend(override.aes = list(size=4)))#+ NoLegend()
p

# ggsave(filename = 'heatMap_Brain1.pdf', plot = p,
#        width = 12.5, height = 7, units = "in", dpi = 1000)

基因symbols和ENSEMBL等ID的相互转化

## 1. transfor Human gene symbols to Ensembl
geneset <- c('AQP4', 'HPCAL1', 'FREM3', 'TRABD2A', 'KRT17',
    'FABP7' , 'ADCYAP1' ,'PVALB',
    'CCK' ,'ENC1','CUX2','RORB','NTNG2','MBP','PCP4',"SNAP25", "MOBP")
suppressPackageStartupMessages(library("org.Hs.eg.db") )

## Warning: package 'BiocGenerics' was built under R version 4.0.5

# remember to install it if you don't have it already
Ensembl <- mapIds(org.Hs.eg.db, keys = geneset, 
                    keytype = "SYMBOL", column="ENSEMBL")

## 'select()' returned 1:many mapping between keys and columns

cat(Ensembl[1:4], '\n')

## ENSG00000171885 ENSG00000115756 ENSG00000183090 ENSG00000186854

# 2. transfor Human gene Ensembl to symbols
Symbol <- mapIds(org.Hs.eg.db, keys = Ensembl, 
                    keytype = "ENSEMBL", column="SYMBOL")

## 'select()' returned 1:many mapping between keys and columns

cat(Symbol[1:4], '\n')

## AQP4 HPCAL1 FREM3 TRABD2A