操作记录-2021-03-04: sunxiaoyu_project

最新推荐文章于 2024-04-17 21:17:24 发布
最新推荐文章于 2024-04-17 21:17:24 发布
阅读量265 收藏
点赞数
分类专栏： 操作记录
版权声明：本文为博主原创文章，遵循 CC 4.0 BY-SA 版权协议，转载请附上原文出处链接和本声明。
本文链接：https://blog.csdn.net/xiaomotong123/article/details/114374988
版权

一、数据加工处理

1. 检查数据完整性

(base) zexing@DNA:~/projects/sunxiaoyu/RNA_seq/2021_03_04$ cat md5.txt > check_md5sum.txt && md5sum -c check_md5sum.txt
./clean/sh4A_2_8_2.clean.fq.gz: OK
./clean/shP2_2_4_2.clean.fq.gz: OK
./clean/shP2_4_2.clean.fq.gz: OK
./clean/shKA_12_2.clean.fq.gz: OK
./clean/shP2_2_N_1.clean.fq.gz: OK
./clean/shP2_2_2.clean.fq.gz: OK
./clean/sh4A_2_4_1.clean.fq.gz: OK
./clean/shP2_2_8_2.clean.fq.gz: OK
./clean/sh4A_2_2_2.clean.fq.gz: OK
./clean/WT_12H_1.clean.fq.gz: OK
./clean/shKA_2_1.clean.fq.gz: OK
./clean/shKA_4_2.clean.fq.gz: OK
./clean/WT2_4H_2.clean.fq.gz: OK
./clean/shKA_4_1.clean.fq.gz: OK
./clean/sP2_2_12_1.clean.fq.gz: OK
./clean/WT2_8H_2.clean.fq.gz: OK
./clean/sh4A_0_1.clean.fq.gz: OK
./clean/shP2_N_2.clean.fq.gz: OK
./clean/shP2_4_1.clean.fq.gz: OK
./clean/WT2_2H_1.clean.fq.gz: OK
./clean/WT_4H_1.clean.fq.gz: OK
./clean/WT2_12H_1.clean.fq.gz: OK
./clean/shP2_2_2_1.clean.fq.gz: OK
./clean/sh4A_0_2.clean.fq.gz: OK
./clean/sh4A_2_8_1.clean.fq.gz: OK
./clean/WT_2H_1.clean.fq.gz: OK
./clean/shP2_2_N_2.clean.fq.gz: OK
./clean/WT_12H_2.clean.fq.gz: OK
./clean/WT2_12H_2.clean.fq.gz: OK
./clean/WT_N_2.clean.fq.gz: OK
./clean/shP2_2_2_2.clean.fq.gz: OK
./clean/WT_2H_2.clean.fq.gz: OK
./clean/shKA_12_1.clean.fq.gz: OK
./clean/sh4A_2_2_1.clean.fq.gz: OK
./clean/shP2_N_1.clean.fq.gz: OK
./clean/shKA_8_1.clean.fq.gz: OK
./clean/shP2_2_4_1.clean.fq.gz: OK
./clean/WT_4H_2.clean.fq.gz: OK
./clean/shP2_8_1.clean.fq.gz: OK
./clean/WT2_8H_1.clean.fq.gz: OK
./clean/shP2_2_8_1.clean.fq.gz: OK
./clean/WT2_4H_1.clean.fq.gz: OK
./clean/WT2_2H_2.clean.fq.gz: OK
./clean/sP2_2_12_2.clean.fq.gz: OK
./clean/shKA_8_2.clean.fq.gz: OK
./clean/shP2_12_1.clean.fq.gz: OK
./clean/WT_N_1.clean.fq.gz: OK
./clean/WT2_N_2.clean.fq.gz: OK
./clean/shP2_8_2.clean.fq.gz: OK
./clean/shP2_12_2.clean.fq.gz: OK
./clean/shKA_2_2.clean.fq.gz: OK
./clean/sh4A_2_4_2.clean.fq.gz: OK
./clean/WT_8H_1.clean.fq.gz: OK
./clean/shP2_2_1.clean.fq.gz: OK
./clean/WT_8H_2.clean.fq.gz: OK
./clean/WT2_N_1.clean.fq.gz: OK
md5sum: WARNING: 1 line is improperly formatted

对有问题的数据重新拷贝。

2. 建立相应目录

# 新建对应的目录
mkdir raw_data clean_data ballgown bam bam_sort sam fastqc_report GSEA MD5_txt  scripts_log

3.在Linux服务器中对RNA_seq数据进行处理

vim新建RNA_seq_script将数据质控、比对、格式转换、排序、拼接和定量综合在一起。

#!/bin/bash
# 上面一行宣告这个script的语法使用bash语法，当程序被执行时，能够载入bash的相关环境配置文件。
# Program
#     This program is used for RNA-seq data analysis.
# History
#     2021/03/04       zexing            First release
# 设置变量${dir}为常用目录
dir=/f/xudonglab/zexing/projects/sunxiaoyu/RNA_seq/2021_03_04

# 对数据进行质控
fastqc -t 16 -o ${dir}/fastqc_report/ ${dir}/clean_data/*.fq.gz

# 利用for循环进行后续操作
for i in  sh4A_0_1 sh4A_12_1 sh4A_12_2 sh4A_2_2 sh4A_4_2 sh4A_8_2 sh4A_N sh4A_N_2_1 shKA_12 shKA_2 shKA_4 shKA_8 shP2_12 shP2_2 shP2_2_2 shP2_2_4 shP2_2_8 shP2_2_N shP2_4 shP2_8 shP2_N shP2_2_12 WT2_12H WT2_2H WT2_4H WT2_8H WT2_N WT_12H WT_2H WT_4H WT_8H WT_N
do
# 对数据进行比对
hisat2 -t -p 16 -x /f/xudonglab/zexing/reference/UCSC_hg19/hisat2_index/hisat2_index_hg19 \
-1 ${dir}/clean_data/${i}_1.clean.fq.gz \
-2 ${dir}/clean_data/${i}_2.clean.fq.gz \
-S ${dir}/sam/${i}.sam

# 对数据进行格式转换
samtools view -@ 16 -S ${dir}/sam/${i}.sam -1b -o ${dir}/bam/${i}.bam

# 对数据进行排序
samtools sort -@ 16 -l 5 -o ${dir}/bam_sort/${i}.bam.sort ${dir}/bam/${i}.bam

# 对数据进行拼接、定量
mkdir ${dir}/ballgown/"$i"
stringtie ${dir}/bam_sort/"$i".bam.sort -o ${dir}/ballgown/"$i"/"$i".gtf \
-p 16 -G /f/xudonglab/zexing/reference/UCSC_hg19/hg19_genes.gtf -e -B \
-A ${dir}/ballgown/"$i"/"$i".gene.tab
done

4. 使用prepDE.py脚本提取read_counts数值

  • 进入ballgown文件夹，将prepDE.py脚本拷贝至当前文件夹
cp /f/xudonglab/zexing/software/prepDE.py ./
  • 退出当前conda环境
conda deactivate
  • 使用python命令直接运行脚本
python prepDE.py

运行结果中"gene_count_matrix.csv"即是DESeq2的输入文件。

二、作图分析

1. 对RNA_seq_2021_03_04绘制热图

# heatmap ----------------------------------------------------------------------
#heatmap绘制时，需要使用gene_symbol和FPKM值
#关于FPKM值的说明
#在绘制heatmap热图时，需要使用差异基因所对应的FPKM值，该值的获取有几个办法：
#利用Stringtie的-A参数直接获得
#利用DESeq2的-FPKM参数由count转化获得
#利用ballgown包进行转化获得
#本次采用StringTie的-A参数直接获得

#关于gene_symbol的说明
#对于绘制heatmap图的gene，使用具有差异性的基因进行绘图
#利用之前DESeq2分析得到的abs(log2FoldChange)>=1的基因来做图
#需要根据"significant_different_genes"来从包含FPKM值的文件中将其提取出来，使用到了match()函数

#绘图前的准备工作

#对FPKM数据进行整理
#清空环境变量
rm(list=ls())
#获取当前工作目录
getwd()

##将StringTie分析得到的含有FPKM数据的TAB文件导入当前工作环境中

#设置工作目录
setwd("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/")

Scr_1_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT_N.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_1_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT_2H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_1_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT_4H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_1_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT_8H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_1_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT_12H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")

Scr_2_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT2_N.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_2_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT2_2H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_2_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT2_4H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_2_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT2_8H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
Scr_2_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/WT2_12H.gene.tab", header = TRUE, sep = "\t" , quote = "\"")

shPRMT2_1_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_N.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_1_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_1_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_4.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_1_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_8.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_1_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_12.gene.tab", header = TRUE, sep = "\t" , quote = "\"")

shPRMT2_2_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2_N.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_2_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_2_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2_4.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_2_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2_8.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shPRMT2_2_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shP2_2_12.gene.tab", header = TRUE, sep = "\t" , quote = "\"")

shKDM4A_1_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_N.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_1_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shKA_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_1_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shKA_4.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_1_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shKA_8.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_1_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/shKA_12.gene.tab", header = TRUE, sep = "\t" , quote = "\"")

shKDM4A_2_0H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_N_2_1.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_2_2H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_2_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_2_4H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_4_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_2_8H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_8_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")
shKDM4A_2_12H.gene.tab <- read.table("G:/sunxiaoyu/RNA-seq/2021_03_04/gene_tab/sh4A_12_2.gene.tab", header = TRUE, sep = "\t" , quote = "\"")


##提取指定列的内容
###对数据中的Gene.ID和FPKM两列数据进行提取
Scr_1_0H.FPKM <- Scr_1_0H.gene.tab[,c(1,8)]
Scr_1_2H.FPKM <- Scr_1_2H.gene.tab[,c(1,8)]
Scr_1_4H.FPKM <- Scr_1_4H.gene.tab[,c(1,8)]
Scr_1_8H.FPKM <- Scr_1_8H.gene.tab[,c(1,8)]
Scr_1_12H.FPKM <- Scr_1_12H.gene.tab[,c(1,8)]

Scr_2_0H.FPKM <- Scr_2_0H.gene.tab[,c(1,8)]
Scr_2_2H.FPKM <- Scr_2_2H.gene.tab[,c(1,8)]
Scr_2_4H.FPKM <- Scr_2_4H.gene.tab[,c(1,8)]
Scr_2_8H.FPKM <- Scr_2_8H.gene.tab[,c(1,8)]
Scr_2_12H.FPKM <- Scr_2_12H.gene.tab[,c(1,8)]

shPRMT2_1_0H.FPKM <- shPRMT2_1_0H.gene.tab[,c(1,8)]
shPRMT2_1_2H.FPKM <- shPRMT2_1_2H.gene.tab[,c(1,8)]
shPRMT2_1_4H.FPKM <- shPRMT2_1_4H.gene.tab[,c(1,8)]
shPRMT2_1_8H.FPKM <- shPRMT2_1_8H.gene.tab[,c(1,8)]
shPRMT2_1_12H.FPKM <- shPRMT2_1_12H.gene.tab[,c(1,8)]

shPRMT2_2_0H.FPKM <- shPRMT2_2_0H.gene.tab[,c(1,8)]
shPRMT2_2_2H.FPKM <- shPRMT2_2_2H.gene.tab[,c(1,8)]
shPRMT2_2_4H.FPKM <- shPRMT2_2_4H.gene.tab[,c(1,8)]
shPRMT2_2_8H.FPKM <- shPRMT2_2_8H.gene.tab[,c(1,8)]
shPRMT2_2_12H.FPKM <- shPRMT2_2_12H.gene.tab[,c(1,8)]

shKDM4A_1_0H.FPKM <- shKDM4A_1_0H.gene.tab[,c(1,8)]
shKDM4A_1_2H.FPKM <- shKDM4A_1_2H.gene.tab[,c(1,8)]
shKDM4A_1_4H.FPKM <- shKDM4A_1_4H.gene.tab[,c(1,8)]
shKDM4A_1_8H.FPKM <- shKDM4A_1_8H.gene.tab[,c(1,8)]
shKDM4A_1_12H.FPKM <- shKDM4A_1_12H.gene.tab[,c(1,8)]

shKDM4A_2_0H.FPKM <- shKDM4A_2_0H.gene.tab[,c(1,8)]
shKDM4A_2_2H.FPKM <- shKDM4A_2_2H.gene.tab[,c(1,8)]
shKDM4A_2_4H.FPKM <- shKDM4A_2_4H.gene.tab[,c(1,8)]
shKDM4A_2_8H.FPKM <- shKDM4A_2_8H.gene.tab[,c(1,8)]
shKDM4A_2_12H.FPKM <- shKDM4A_2_12H.gene.tab[,c(1,8)]


###重命名指定列
###重命名全部的列是name(data) <- c("NO","name")
###重命名单个列是colnames(data)[2] <- 'newname'
colnames(Scr_1_0H.FPKM)[2] <-"Scr_1_0H"
colnames(Scr_1_2H.FPKM)[2] <-"Scr_1_2H"
colnames(Scr_1_4H.FPKM)[2] <-"Scr_1_4H"
colnames(Scr_1_8H.FPKM)[2] <-"Scr_1_8H"
colnames(Scr_1_12H.FPKM)[2] <-"Scr_1_12H"

colnames(Scr_2_0H.FPKM)[2] <-"Scr_2_0H"
colnames(Scr_2_2H.FPKM)[2] <-"Scr_2_2H"
colnames(Scr_2_4H.FPKM)[2] <-"Scr_2_4H"
colnames(Scr_2_8H.FPKM)[2] <-"Scr_2_8H"
colnames(Scr_2_12H.FPKM)[2] <-"Scr_2_12H"

colnames(shPRMT2_1_0H.FPKM)[2] <-"shPRMT2_1_0H"
colnames(shPRMT2_1_2H.FPKM)[2] <-"shPRMT2_1_2H"
colnames(shPRMT2_1_4H.FPKM)[2] <-"shPRMT2_1_4H"
colnames(shPRMT2_1_8H.FPKM)[2] <-"shPRMT2_1_8H"
colnames(shPRMT2_1_12H.FPKM)[2] <-"shPRMT2_1_12H"

colnames(shPRMT2_2_0H.FPKM)[2] <-"shPRMT2_2_0H"
colnames(shPRMT2_2_2H.FPKM)[2] <-"shPRMT2_2_2H"
colnames(shPRMT2_2_4H.FPKM)[2] <-"shPRMT2_2_4H"
colnames(shPRMT2_2_8H.FPKM)[2] <-"shPRMT2_2_8H"
colnames(shPRMT2_2_12H.FPKM)[2] <-"shPRMT2_2_12H"

colnames(shKDM4A_1_0H.FPKM)[2] <-"shKDM4A_1_0H"
colnames(shKDM4A_1_2H.FPKM)[2] <-"shKDM4A_1_2H"
colnames(shKDM4A_1_4H.FPKM)[2] <-"shKDM4A_1_4H"
colnames(shKDM4A_1_8H.FPKM)[2] <-"shKDM4A_1_8H"
colnames(shKDM4A_1_12H.FPKM)[2] <-"shKDM4A_1_12H"

colnames(shKDM4A_2_0H.FPKM)[2] <-"shKDM4A_2_0H"
colnames(shKDM4A_2_2H.FPKM)[2] <-"shKDM4A_2_2H"
colnames(shKDM4A_2_4H.FPKM)[2] <-"shKDM4A_2_4H"
colnames(shKDM4A_2_8H.FPKM)[2] <-"shKDM4A_2_8H"
colnames(shKDM4A_2_12H.FPKM)[2] <-"shKDM4A_2_12H"

##将得到的各样本的FPKM值数据保存入heatmap目录
write.table(Scr_1_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_1_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_1_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_1_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_1_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_1_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_1_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_1_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_1_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_1_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

write.table(Scr_2_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_2_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_2_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_2_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_2_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_2_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_2_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_2_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(Scr_2_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/Scr_2_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

write.table(shPRMT2_1_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_1_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_1_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_1_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_1_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_1_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_1_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_1_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_1_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_1_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

write.table(shPRMT2_2_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_2_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_2_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_2_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_2_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_2_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_2_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_2_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shPRMT2_2_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shPRMT2_2_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

write.table(shKDM4A_1_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_1_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_1_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_1_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_1_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_1_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_1_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_1_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_1_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_1_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

write.table(shKDM4A_2_0H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_2_0H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_2_2H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_2_2H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_2_4H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_2_4H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_2_8H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_2_8H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")
write.table(shKDM4A_2_12H.FPKM, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/shKDM4A_2_12H.FPKM", row.names = FALSE, quote = FALSE, sep = "\t")

# 对所有样品的FPKM进行合并

#使用intersect函数选取各个样品中的共有gene_id

##intersect函数处理的是两个向量的交集，需要先将gene_id转换成字符向量
Scr_1_0H_gene <- Scr_1_0H.FPKM$Gene.ID
Scr_1_2H_gene <- Scr_1_2H.FPKM$Gene.ID
Scr_1_4H_gene <- Scr_1_4H.FPKM$Gene.ID
Scr_1_8H_gene <- Scr_1_8H.FPKM$Gene.ID
Scr_1_12H_gene <- Scr_1_12H.FPKM$Gene.ID

Scr_2_0H_gene <- Scr_2_0H.FPKM$Gene.ID
Scr_2_2H_gene <- Scr_2_2H.FPKM$Gene.ID
Scr_2_4H_gene <- Scr_2_4H.FPKM$Gene.ID
Scr_2_8H_gene <- Scr_2_8H.FPKM$Gene.ID
Scr_2_12H_gene <- Scr_2_12H.FPKM$Gene.ID

shPRMT2_1_0H_gene <- shPRMT2_1_0H.FPKM$Gene.ID
shPRMT2_1_2H_gene <- shPRMT2_1_2H.FPKM$Gene.ID
shPRMT2_1_4H_gene <- shPRMT2_1_4H.FPKM$Gene.ID
shPRMT2_1_8H_gene <- shPRMT2_1_8H.FPKM$Gene.ID
shPRMT2_1_12H_gene <- shPRMT2_1_12H.FPKM$Gene.ID

shPRMT2_2_0H_gene <- shPRMT2_2_0H.FPKM$Gene.ID
shPRMT2_2_2H_gene <- shPRMT2_2_2H.FPKM$Gene.ID
shPRMT2_2_4H_gene <- shPRMT2_2_4H.FPKM$Gene.ID
shPRMT2_2_8H_gene <- shPRMT2_2_8H.FPKM$Gene.ID
shPRMT2_2_12H_gene <- shPRMT2_2_12H.FPKM$Gene.ID

shKDM4A_1_0H_gene <- shKDM4A_1_0H.FPKM$Gene.ID
shKDM4A_1_2H_gene <- shKDM4A_1_2H.FPKM$Gene.ID
shKDM4A_1_4H_gene <- shKDM4A_1_4H.FPKM$Gene.ID
shKDM4A_1_8H_gene <- shKDM4A_1_8H.FPKM$Gene.ID
shKDM4A_1_12H_gene <- shKDM4A_1_12H.FPKM$Gene.ID

shKDM4A_2_0H_gene <- shKDM4A_2_0H.FPKM$Gene.ID
shKDM4A_2_2H_gene <- shKDM4A_2_2H.FPKM$Gene.ID
shKDM4A_2_4H_gene <- shKDM4A_2_4H.FPKM$Gene.ID
shKDM4A_2_8H_gene <- shKDM4A_2_8H.FPKM$Gene.ID
shKDM4A_2_12H_gene <- shKDM4A_2_12H.FPKM$Gene.ID

##使用intersect函数选取各个样品中的共有gene_id
Scr_1_common_gene_1 <- intersect(Scr_1_0H_gene, Scr_1_2H_gene)
Scr_1_common_gene_2 <- intersect(Scr_1_common_gene_1, Scr_1_4H_gene)
Scr_1_common_gene_3 <- intersect(Scr_1_common_gene_2, Scr_1_8H_gene)
Scr_1_common_gene_4 <- intersect(Scr_1_common_gene_3, Scr_1_12H_gene)

Scr_2_common_gene_1 <- intersect(Scr_2_0H_gene, Scr_2_2H_gene)
Scr_2_common_gene_2 <- intersect(Scr_2_common_gene_1, Scr_2_4H_gene)
Scr_2_common_gene_3 <- intersect(Scr_2_common_gene_2, Scr_2_8H_gene)
Scr_2_common_gene_4 <- intersect(Scr_2_common_gene_3, Scr_2_12H_gene)

shPRMT2_1_common_gene_1 <- intersect(shPRMT2_1_0H_gene, shPRMT2_1_2H_gene)
shPRMT2_1_common_gene_2 <- intersect(shPRMT2_1_common_gene_1, shPRMT2_1_4H_gene)
shPRMT2_1_common_gene_3 <- intersect(shPRMT2_1_common_gene_2, shPRMT2_1_8H_gene)
shPRMT2_1_common_gene_4 <- intersect(shPRMT2_1_common_gene_3, shPRMT2_1_12H_gene)

shPRMT2_2_common_gene_1 <- intersect(shPRMT2_2_0H_gene, shPRMT2_2_2H_gene)
shPRMT2_2_common_gene_2 <- intersect(shPRMT2_2_common_gene_1, shPRMT2_2_4H_gene)
shPRMT2_2_common_gene_3 <- intersect(shPRMT2_2_common_gene_2, shPRMT2_2_8H_gene)
shPRMT2_2_common_gene_4 <- intersect(shPRMT2_2_common_gene_3, shPRMT2_2_12H_gene)

shKDM4A_1_common_gene_1 <- intersect(shKDM4A_1_0H_gene, shKDM4A_1_2H_gene)
shKDM4A_1_common_gene_2 <- intersect(shKDM4A_1_common_gene_1, shKDM4A_1_4H_gene)
shKDM4A_1_common_gene_3 <- intersect(shKDM4A_1_common_gene_2, shKDM4A_1_8H_gene)
shKDM4A_1_common_gene_4 <- intersect(shKDM4A_1_common_gene_3, shKDM4A_1_12H_gene)

shKDM4A_2_common_gene_1 <- intersect(shKDM4A_2_0H_gene, shKDM4A_2_2H_gene)
shKDM4A_2_common_gene_2 <- intersect(shKDM4A_2_common_gene_1, shKDM4A_2_4H_gene)
shKDM4A_2_common_gene_3 <- intersect(shKDM4A_2_common_gene_2, shKDM4A_2_8H_gene)
shKDM4A_2_common_gene_4 <- intersect(shKDM4A_2_common_gene_3, shKDM4A_2_12H_gene)

common_gene_1 <- intersect(Scr_1_common_gene_4, Scr_2_common_gene_4)
common_gene_2 <- intersect(common_gene_1, shPRMT2_1_common_gene_4)
common_gene_3 <- intersect(common_gene_2, shPRMT2_2_common_gene_4)
common_gene_4 <- intersect(common_gene_3, shKDM4A_1_common_gene_4)
common_gene_5 <- intersect(common_gene_1, shKDM4A_2_common_gene_4)

#利用match函数对共有基因List信息（小文件）和FPKM值信息（大文件）进行提取
##利用match函数提取各样品中差异基因所在的行数并重新命名为row.NO文件
##match(x,y)函数输出结果：x向量在y向量中所处的位置，x向量元素不存在y向量中的返回NA
##match(x, table$i)函数输出结果：返回x向量在table中$i列中所处的位置
##利用common_gene对各样品进行处理
Scr_1_0H_common_gene_row.NO <- c(match(common_gene_5, Scr_1_0H.FPKM$Gene.ID))
Scr_1_2H_common_gene_row.NO <- c(match(common_gene_5, Scr_1_2H.FPKM$Gene.ID))
Scr_1_4H_common_gene_row.NO <- c(match(common_gene_5, Scr_1_4H.FPKM$Gene.ID))
Scr_1_8H_common_gene_row.NO <- c(match(common_gene_5, Scr_1_8H.FPKM$Gene.ID))
Scr_1_12H_common_gene_row.NO <- c(match(common_gene_5, Scr_1_12H.FPKM$Gene.ID))

Scr_2_0H_common_gene_row.NO <- c(match(common_gene_5, Scr_2_0H.FPKM$Gene.ID))
Scr_2_2H_common_gene_row.NO <- c(match(common_gene_5, Scr_2_2H.FPKM$Gene.ID))
Scr_2_4H_common_gene_row.NO <- c(match(common_gene_5, Scr_2_4H.FPKM$Gene.ID))
Scr_2_8H_common_gene_row.NO <- c(match(common_gene_5, Scr_2_8H.FPKM$Gene.ID))
Scr_2_12H_common_gene_row.NO <- c(match(common_gene_5, Scr_2_12H.FPKM$Gene.ID))

shPRMT2_1_0H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_1_0H.FPKM$Gene.ID))
shPRMT2_1_2H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_1_2H.FPKM$Gene.ID))
shPRMT2_1_4H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_1_4H.FPKM$Gene.ID))
shPRMT2_1_8H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_1_8H.FPKM$Gene.ID))
shPRMT2_1_12H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_1_12H.FPKM$Gene.ID))

shPRMT2_2_0H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_2_0H.FPKM$Gene.ID))
shPRMT2_2_2H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_2_2H.FPKM$Gene.ID))
shPRMT2_2_4H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_2_4H.FPKM$Gene.ID))
shPRMT2_2_8H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_2_8H.FPKM$Gene.ID))
shPRMT2_2_12H_common_gene_row.NO <- c(match(common_gene_5, shPRMT2_2_12H.FPKM$Gene.ID))

shKDM4A_1_0H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_1_0H.FPKM$Gene.ID))
shKDM4A_1_2H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_1_2H.FPKM$Gene.ID))
shKDM4A_1_4H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_1_4H.FPKM$Gene.ID))
shKDM4A_1_8H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_1_8H.FPKM$Gene.ID))
shKDM4A_1_12H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_1_12H.FPKM$Gene.ID))

shKDM4A_2_0H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_2_0H.FPKM$Gene.ID))
shKDM4A_2_2H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_2_2H.FPKM$Gene.ID))
shKDM4A_2_4H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_2_4H.FPKM$Gene.ID))
shKDM4A_2_8H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_2_8H.FPKM$Gene.ID))
shKDM4A_2_12H_common_gene_row.NO <- c(match(common_gene_5, shKDM4A_2_12H.FPKM$Gene.ID))

#根据以上行数，对各样品的FPKM值进行提取
##利用common_gene对各样品的FPKM值进行提取

Scr_1_0H_common_gene_FPKM <- Scr_1_0H.FPKM[Scr_1_0H_common_gene_row.NO ,]
Scr_1_2H_common_gene_FPKM <- Scr_1_2H.FPKM[Scr_1_2H_common_gene_row.NO ,]
Scr_1_4H_common_gene_FPKM <- Scr_1_4H.FPKM[Scr_1_4H_common_gene_row.NO ,]
Scr_1_8H_common_gene_FPKM <- Scr_1_8H.FPKM[Scr_1_8H_common_gene_row.NO ,]
Scr_1_12H_common_gene_FPKM <- Scr_1_12H.FPKM[Scr_1_12H_common_gene_row.NO ,]

Scr_2_0H_common_gene_FPKM <- Scr_2_0H.FPKM[Scr_2_0H_common_gene_row.NO ,]
Scr_2_2H_common_gene_FPKM <- Scr_2_2H.FPKM[Scr_2_2H_common_gene_row.NO ,]
Scr_2_4H_common_gene_FPKM <- Scr_2_4H.FPKM[Scr_2_4H_common_gene_row.NO ,]
Scr_2_8H_common_gene_FPKM <- Scr_2_8H.FPKM[Scr_2_8H_common_gene_row.NO ,]
Scr_2_12H_common_gene_FPKM <- Scr_2_12H.FPKM[Scr_2_12H_common_gene_row.NO ,]


shPRMT2_1_0H_common_gene_FPKM <- shPRMT2_1_0H.FPKM[shPRMT2_1_0H_common_gene_row.NO ,]
shPRMT2_1_2H_common_gene_FPKM <- shPRMT2_1_2H.FPKM[shPRMT2_1_2H_common_gene_row.NO ,]
shPRMT2_1_4H_common_gene_FPKM <- shPRMT2_1_4H.FPKM[shPRMT2_1_4H_common_gene_row.NO ,]
shPRMT2_1_8H_common_gene_FPKM <- shPRMT2_1_8H.FPKM[shPRMT2_1_8H_common_gene_row.NO ,]
shPRMT2_1_12H_common_gene_FPKM <- shPRMT2_1_12H.FPKM[shPRMT2_1_12H_common_gene_row.NO ,]

shPRMT2_2_0H_common_gene_FPKM <- shPRMT2_2_0H.FPKM[shPRMT2_2_0H_common_gene_row.NO ,]
shPRMT2_2_2H_common_gene_FPKM <- shPRMT2_2_2H.FPKM[shPRMT2_2_2H_common_gene_row.NO ,]
shPRMT2_2_4H_common_gene_FPKM <- shPRMT2_2_4H.FPKM[shPRMT2_2_4H_common_gene_row.NO ,]
shPRMT2_2_8H_common_gene_FPKM <- shPRMT2_2_8H.FPKM[shPRMT2_2_8H_common_gene_row.NO ,]
shPRMT2_2_12H_common_gene_FPKM <- shPRMT2_2_12H.FPKM[shPRMT2_2_12H_common_gene_row.NO ,]

shKDM4A_1_0H_common_gene_FPKM <- shKDM4A_1_0H.FPKM[shKDM4A_1_0H_common_gene_row.NO ,]
shKDM4A_1_2H_common_gene_FPKM <- shKDM4A_1_2H.FPKM[shKDM4A_1_2H_common_gene_row.NO ,]
shKDM4A_1_4H_common_gene_FPKM <- shKDM4A_1_4H.FPKM[shKDM4A_1_4H_common_gene_row.NO ,]
shKDM4A_1_8H_common_gene_FPKM <- shKDM4A_1_8H.FPKM[shKDM4A_1_8H_common_gene_row.NO ,]
shKDM4A_1_12H_common_gene_FPKM <- shKDM4A_1_12H.FPKM[shKDM4A_1_12H_common_gene_row.NO ,]

shKDM4A_2_0H_common_gene_FPKM <- shKDM4A_2_0H.FPKM[shKDM4A_2_0H_common_gene_row.NO ,]
shKDM4A_2_2H_common_gene_FPKM <- shKDM4A_2_2H.FPKM[shKDM4A_2_2H_common_gene_row.NO ,]
shKDM4A_2_4H_common_gene_FPKM <- shKDM4A_2_4H.FPKM[shKDM4A_2_4H_common_gene_row.NO ,]
shKDM4A_2_8H_common_gene_FPKM <- shKDM4A_2_8H.FPKM[shKDM4A_2_8H_common_gene_row.NO ,]
shKDM4A_2_12H_common_gene_FPKM <- shKDM4A_2_12H.FPKM[shKDM4A_2_12H_common_gene_row.NO ,]

##利用Merge函数对各样品的FPKM值进行合并
Scr_1_common_gene_FPKM <- merge(Scr_1_0H_common_gene_FPKM, merge(merge(Scr_1_2H_common_gene_FPKM,Scr_1_4H_common_gene_FPKM, by="Gene.ID"), merge(Scr_1_8H_common_gene_FPKM,Scr_1_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")
Scr_2_common_gene_FPKM <- merge(Scr_2_0H_common_gene_FPKM, merge(merge(Scr_2_2H_common_gene_FPKM,Scr_2_4H_common_gene_FPKM, by="Gene.ID"), merge(Scr_2_8H_common_gene_FPKM,Scr_2_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")

shPRMT2_1_common_gene_FPKM <- merge(shPRMT2_1_0H_common_gene_FPKM, merge(merge(shPRMT2_1_2H_common_gene_FPKM,shPRMT2_1_4H_common_gene_FPKM, by="Gene.ID"), merge(shPRMT2_1_8H_common_gene_FPKM,shPRMT2_1_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")
shPRMT2_2_common_gene_FPKM <- merge(shPRMT2_2_0H_common_gene_FPKM, merge(merge(shPRMT2_2_2H_common_gene_FPKM,shPRMT2_2_4H_common_gene_FPKM, by="Gene.ID"), merge(shPRMT2_2_8H_common_gene_FPKM,shPRMT2_2_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")

shKDM4A_1_common_gene_FPKM <- merge(shKDM4A_1_0H_common_gene_FPKM, merge(merge(shKDM4A_1_2H_common_gene_FPKM,shKDM4A_1_4H_common_gene_FPKM, by="Gene.ID"), merge(shKDM4A_1_8H_common_gene_FPKM,shKDM4A_1_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")
shKDM4A_2_common_gene_FPKM <- merge(shKDM4A_2_0H_common_gene_FPKM, merge(merge(shKDM4A_2_2H_common_gene_FPKM,shKDM4A_2_4H_common_gene_FPKM, by="Gene.ID"), merge(shKDM4A_2_8H_common_gene_FPKM,shKDM4A_2_12H_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")

common_gene_FPKM <- merge(merge(Scr_1_common_gene_FPKM, Scr_2_common_gene_FPKM, by="Gene.ID"), merge(merge(shPRMT2_1_common_gene_FPKM, shPRMT2_2_common_gene_FPKM, by="Gene.ID"), merge(shKDM4A_1_common_gene_FPKM, shKDM4A_2_common_gene_FPKM, by="Gene.ID"), by="Gene.ID"), by="Gene.ID")

#将gene_id作为文件的行名
rownames(common_gene_FPKM) <- common_gene_FPKM[,1]
common_gene_FPKM <- common_gene_FPKM[,-1]

#将FPKM值均为0的基因进行剔除
fpkm <- common_gene_FPKM[rowSums(common_gene_FPKM>0)>0 , ]

##将得到的各样本的FPKM值数据保存入heatmap目录
write.table(fpkm, file = "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/fpkm.txt", row.names = TRUE, quote = FALSE, sep = "\t")

write.csv(fpkm, "G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/fpkm.csv", quote = FALSE, row.names = TRUE)

#pheatmap绘图
results <- read.csv("G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/fpkm.csv", row.names = 1,header = T)
#加载包
library(RColorBrewer)#设置颜色用的
# BiocManager::install("pheatmap")
library(pheatmap)
#设置配色方案
cc = colorRampPalette(rev(brewer.pal(n=7, name="RdYlBu"))) #Rd=red Yl=yellow Bu=blue

#如果矩阵内容是fpkm表达量，一般取log10(fpkm+1)绘图
results=log2(results+1)

#pheatmap参数解释：
#第一个参数是需要用pheatmap画图的数据
#color: 设置颜色。如果想画得更精细一些，可以取cc(1000)
#main: 标题，会显示在最上面
#fontsize: row的字体大小
#scale: 是否归一化为正态分布，可选row,column,none。一般对row进行归一化的情况比较多，column较少。
#border_color: 是否显示边框及边框的颜色，NA不显示, red显示红色。支持简单的颜色单词
#na_col: 设置缺失值的颜色，支持简单颜色单词，一般设置为灰色就满好识别的。
#cluster_rows & cluster_cols: 设置是否对行进行聚类，这个就见仁见智，看你的实际需求了。当缺失值较多的时候是无法进行聚类的。一个解决办法是读取数据的时候不设置缺失值。
#show_rownames & show_colnames: 是否显示行/列的名称
#treeheight_row & treeheight_col: 当前面设置了聚类之后，两边会出现聚类的树，这个参数是设置树的高度的。
#cellheight & cellwidth: 设置每个各自的宽度和高度。有的时候不设置这两个值画出来的树容易放飞自我????
#cutree_row & cutree_col: 是否根据聚类情况把树切开，可以设置切开的份数。
#display_numbers: 设置是否显示每个单元格的值。这个也是个人喜好及文章需求。
#legend: 设置是否显示旁边的bar状图例，emmmm好像还没碰到说不要那个玩意儿的情况。。
#filename: 设置输出文件的名字。可以设置的文件类型有：pdf，png，jpg，tiff，bmp

#设置工作目录
setwd("G:/sunxiaoyu/RNA-seq/2021_03_04/Rtreatment/heatmap/")

heatmap = pheatmap(results, color = colorRampPalette(c("blue", "white", "red"))(1000),
                   main=" ",
                   fontsize = 4,                               # 字体大小
                   scale="row",                             # 比例尺依据？
                   border_color = NA,                          # 边框颜色
                   na_col = " ",
                   cluster_rows = T,cluster_cols = F,          # 聚类行，聚类列
                   show_rownames = T,show_colnames = T,        # 显示行名称，显示列名称   
                   treeheight_row = 50, treeheight_col = 50,
                   cellheight = 5, cellwidth = 5,
                   cutree_row=1, cutree_col=1,
                   display_numbers = F,legend = T,
                   filename = "Result_2.tiff")

#绘图group_up
heatmap=pheatmap(results,color = cc(1000),
                 main=" ",
                 fontsize = 15,
                 scale="row",
                 border_color = NA,
                 na_col = "grey",
                 cluster_rows = F,cluster_cols = F,
                 show_rownames = T,show_colnames = T,
                 treeheight_row = 30,treeheight_col = 3,
                 cellheight = 3,cellwidth = 3,
                 cutree_row=1,cutree_col=1,
                 display_numbers = F,legend = T,
                 filename = "results_2.tiff")
垚垚爸爱学习
关注
  • 0
    点赞
  • 踩
  • 0
    收藏
    觉得还不错? 一键收藏
  • 1
    评论
专栏目录
操作记录-2020-11-08：精简代码处理RNA_seq数据
垚垚爸的博客
11-08 2831
今天准备尝试编写一组精简代码用于处理RNA_seq数据，希望能成功吧。 1.建立相应目录 对新数据建立对应实验人员（lizexing）、测序类型（RNA_seq）和日期（2020_10_20）的目录。 # 建立后如下： (base) zexing@DNA:~/projects/lizexing/RNA_seq/2020_11_08$ # 新建对应的各级目录 mkdir raw_data clean_data ballgown bam bam_sort sam fastqc_report GSEA MD5_
webbrowser1 脚本报错_HISAT2+Stringtie+DESeq2 （prepDE.py脚本报错向)
weixin_29817925的博客
12-20 1011
2019/10/14 原作者出了解决方案，更新了prepDE.py脚本。=====================原文==============================写这篇文章的主要原因还是出于这两天来找一个很小的bug找不到，最后发现版本不兼容的故事。背景：HISAT2+Stringtie+Ballgown本来是一组黄金组合，但是由于我的生物学重复（biological replic...
Stringtie 计算转录组的 Raw Counts
公众号/简说基因，知乎/简宝玉
03-20 1944
Stringtie 自带一个脚本prepDE.py用于计算转录组的 Raw Counts，用法如下：Usage: prepDE.py [options] Generates two CS...
转录组上游分析，Count计算
最新发布
BioinfoDu
04-17 1414
featureCounts是subread中脚本，可以使用subread流程进行定量，在这里直接使用前面mapped的bam文件进行转录本定量。，主要发表或收录生物信息学的教程，以及基于R的分析和可视化（包括数据分析，图形绘制等）；因此，个人建议仍是获得count值，后再进一步的分析，这样的方法更利于下游分析。是stringtie软件中自带的获得转录本丰度的脚本，6.1中的。文件进行转录本表达量的比对，获得转录本的FPKM，此后使用。在网络中吗，都有比较详细的教程，大家可以自己去学习。
RNA-seq流程学习笔记（17）- PCA图聚类分析
垚垚爸的博客
03-25 7641
#绘制PCA图 #需要使用各组的FPKM进行绘制 #对FPKM数据进行整理 #清空环境变量 rm(list=ls()) ##将StringTie分析得到的含有FPKM数据的TAB文件导入当前工作环境中 #设置工作目录 setwd("G:/kongyu/RNA-seq/2021_02_22/gene_tab/") DIPG4_1_1.gene.tab <- read.table("G:/kongyu/RNA-seq/2021_02_22/gene_tab/DIPG4_1_1.gene.tab",
03继电保护实验指导书.doc
06-09
3. DH-3型三相一次重合闸装置实验，让学生实际操作重合闸装置，体验其工作过程。 4. 自动重合闸前加速保护实验，涉及在不同情况下如何快速响应并恢复供电。 5. 重复动作手动/自动复归中央信号装置实验，关注的是信号...
操作记录-2022-09-12: xieruyu_project
垚垚爸的博客
09-12 707
鸡的转录基因组分析
2021-07-14:sunruiqi_RNA_seq
垚垚爸的博客
07-15 503
今天准备尝试编写一组精简代码用于处理RNA_seq数据，希望能成功吧。 1.建立相应目录 对新数据建立对应实验人员（sunruiqi）、测序类型（RNA_seq）和日期（2021_07_14）的目录。 # 建立后如下： (base) zexing@bio:~/projects/sunruiqi/RNA_seq/2021_07_14$ # 新建对应的目录 mkdir raw_data clean_data ballgown bam bam_sort sam fastqc_report GSEA MD5_tx
signature=afa01c88c54d50cbb031be121a63b5d9,fomo3d_simple/yarn.lock at master · MajorTom404/fomo3d_si...
weixin_33162074的博客
05-30 2万+
# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.# yarn lockfile v1"@babel/runtime@^7.3.1":version "7.3.1"resolved "http://registry.npm.taobao.org/@babel/runtime/download/@babel/runtime...
signature=a20b3c3a6ff607accc831e6d492695f4,qfinance-token/yarn.lock at master · QFinanceDeFi/qfinanc...
热门推荐
weixin_35317737的博客
05-30 6万+
# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.# yarn lockfile v1"@babel/helper-module-imports@^7.12.1":version "7.12.5"resolved "https://registry.yarnpkg.com/@babel/helper-module-imp...
Linux的RNA-seq分析（stringtie-FPKM和HTseq计数）
weixin_43927366的博客
03-15 1569
确保安装了stringtie如果要研究新的转录本，则需要完成所有样本的转录本的组装并整合在stingtie-merged.gtf中，详细见Linux系统RNA-seq分析（stringtie转录本组装)。新建SRR3418005_FPKM子文件夹，并在其中打开终端：这个选项告诉stringtie不仅要输出组装得到的转录本，还要输出那些表达量较低、可能不被认为是完整转录本的“额外”转录本片段。这有助于捕获那些可能只部分被测序覆盖的转录本区域。-p 2：这个选项指定了stringtie。
生信步骤|转录组测序上游分析：hisat2+samtools+stringtie
学术程稻属
01-12 7027
转录组分析在当下研究功能基因组领域十分常用。相关软件组合种类也十分丰富，本文采用了hisat2+samtools+stringtie策略从转录组数据中挖掘差异表达基因。在这里小编整理了一下此套组合的执行流程，以供日后查阅；同时分享在平台，如果能帮助到更多初学者，小编将不甚荣幸，如有谬误也希望各路大佬批评指正。 先从整体上看一下软件们所执行的功能： hisat2：建立参考基因组索引，reads的比对 samtools：sam2bam的转化 stringtie：估算转录本表达量
mapping、bam结果提取、覆盖率、数据深度、序列拼接
Curry_chenhu的博客
07-25 3400
提取比对到参考序列结果 samtools view -bF 4 abc.bam > abc.F.bam 配对比对 samtools view -bF 12 abc.bam > abc.F.bam #bam排序 samtools sort *.bam -o *.bam bam转fq bedtools bamtofastq -i * -fq *_1.fq -fq2 *_2.fq samtools fastq NOf41_human-mapped.bam > NOf41_human_test.f
QT压缩和解压ZIP学习笔记二：编译quazip 32位和64位dll
yxy244的博客
03-22 1353
QuaZIP是使用Qt/C++对ZLIB进行简单封装的用于压缩及解压缩ZIP的开源库。适用于多种平台，利用它可以很方便的将单个或多个文件打包为zip文件，且打包后的zip文件可以通过其它工具打开。 QuaZIP下载 https://github.com/stachenov/quazip QT编译quazip根据编译器不同，MSVC和MinGW步骤不一样，这也是为照着网上步骤，有的成...
HISAT2+StringTie+Ballgown安装及使用流程
weixin_30415113的博客
11-09 2085
HISAT2+StringTie+Ballgown安装及使用流程 2015年Nature Methods上面发表了一款快速比对工具hisat，作为接替tophat和bowtie的比对工具，它具有更快的比对速度和更高的比对率，最近把这个流程走完一遍，感觉优势还是很明显的。一、HISAT2：1、下载安装：hisat2下载地址：ftp://ftp.ccb.jhu.edu/pub/infphilo...
操作记录-2020-12-21: dongfeng_GAS_project
垚垚爸的博客
01-04 949
今天老菜鸟接了实验室一个大活，要帮学生把一个课题结掉，因此需要处理三批次数据。当然了，老菜鸟这些天正在忙一些其他事情，不知道这些事情有了结果后，还会不会再继续这些工作了，暂且记录一下自己目前复杂的心情吧。 1. 建立相应目录 # 新建对应的目录 mkdir raw_data clean_data ballgown bam bam_sort sam fastqc_report GSEA MD5_txt scripts_log 2. 检查数据完整性 这次将提供的md5.txt中数据提前编辑了一下，修改了样品
操作记录-2020-09-27：xiaxianyou_RNA_seq
垚垚爸的博客
09-27 1039
1. 检查上传数据的完整性 操作记录如下： #显示各数据的完整性代码 (base) zexing@DNA:~/projects/xiaxianyou/RNA_seq/2020_09_23/cleandata$ cat *.txt ea24c0a81c3b146f52180d03fb387f54 s4301_FKDL202588235-1a_1.clean.fq.gz 44e7699dc34c62f7947e4288ea1f0f72 s4301_FKDL202588235-1a_2.clean.fq.gz
操作记录-2021-03-15: sunxiaoyu_project
垚垚爸的博客
03-15 256
1、数据处理记录 【1】使用网页另存为将数据文件保存至本地电脑后，上传至服务器中 【2】利用SRAtoolkits中的fastq-dump命令，将SRA数据转换为fastq格式 #命令如下： (base) zexing@DNA:~/projects/sunxiaoyu/RNA_seq/2021_03_15/clean_data$ fastq-dump --split-e SRR11906971 SRR11906972 SRR11906973 SRR11906974 Read 27386449 spots f

“相关推荐”对你有帮助么？

  • 非常没帮助
  • 没帮助
  • 一般
  • 有帮助
  • 非常有帮助
提交
评论 1
添加红包

请填写红包祝福语或标题

个

红包个数最小为10个

元

红包金额最低5元

当前余额3.43元 前往充值 >
需支付：10.00元
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包
实付元
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明：

1.余额是钱包充值的虚拟货币，按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载，可以购买VIP、付费专栏及课程。

余额充值