在我们的shiny服务器部署一个RNA-seq下游分析网页工具

rm(list = ls()) 
options()$repos 
options()$BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options()$repos 
options()$BioC_mirror

if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")

BiocManager::install(c("rhdf5","tximport",'DESeq2','clusterProfiler',"org.Hs.eg.db","org.Mm.eg.db","org.Mmu.eg.db","sva","limma","geneplotter",'biomaRt',"pcaGoPromoter","pcaGoPromoter.Mm.mm9","pcaGoPromoter.Hs.hg19","pathview"))

BiocManager::install(c("shiny","shinyBS","shinyjs",'RColorBrewer',"stringr",'formula.tools','data.table','fdrtool',"VennDiagram",'colorspace',"xlsx",'svglite',"visNetwork","V8","ggrepel","ReporteRs","ReporteRsjars"))

install.packages("gplots",dependencies = TRUE)
install.packages("plotly")
install.packages("devtools") 
install.packages("WGCNA") 
devtools::install_github("rstudio/crosstalk",force=TRUE)

mkdir -p /srv/shiny-server/paper
cd /srv/shiny-server/paper
git clone https://github.com/szenitha/Shiny-Seq.git

 ls *.R|while read id;do( mv  $id  ${id/.R/.r});done

 sudo systemctl restart shiny-server

sample    group   stage   grade   passages
SCBO.5_orgP10    organoids    T1+CIS  Hg 10
SCBO.5_orgP13    organoids    T1+CIS  Hg 13
SCBO.1_orgP7    organoids    Ta  Hg 7
SCBO.3_orgP4    organoids    T1  Lg/Hg  4
SCBO.6_orgP4    organoids    T1+CIS  Hg 4
SCBO.2_orgP5    organoids    T2  Lg/Hg  5
SCBO.4_orgP10    organoids    T2  Hg 10
SCBO.5_orgP3    organoids    T1+CIS  Hg 3

filepath='~/Downloads/2018-bladder-organoids-counts.txt'
input_exp<-read.csv(filepath, header = TRUE,sep = "\t",check.names = FALSE,quote = "\"")
data<-input_exp[,-1]

#convert entries to integers
data=as.matrix(data)
storage.mode(data)="double"
data= data.frame(data)
rownames(data)=input_exp[,1]

get_pheno<-function(data,pheno)
{
  #Expression table and annotation table should not be null
  if(!is.null(data) && !is.null(pheno))
  {

    #Assuming that the first column of annotation table is sample id ,extract all sample IDs
    sample_id = pheno[,1]
    #print(sample_id)
    #Get all sample IDs from expression table(sample ID refer to column names of expression table)
    exp_sample_id = colnames(data)
    #print('all')
    # print(exp_sample_id)
    #Check if all sample ID in expression table are present in the annotation table
    if (all(exp_sample_id %in% sample_id))
    {
      #print("Yay")

      #set all variables of annotation table as factors
      col<-1:ncol(pheno)
      for (i in col)
      {
        pheno[,i]<-as.factor(pheno[,i])
      }
      #Remove those sample IDs that are present in the expression table but absent in the annotation table from the annotation table
      idx<-NULL
      if(!all(sample_id %in% exp_sample_id))
      {
        idx<-which(!(sample_id %in% exp_sample_id))
        pheno <- pheno[-idx, ]
      }

      pheno<-pheno

    }
    else 
    {
      pheno<-NULL
      #print('nay')

    }
    return(pheno)
  }
}


input_p<-read.csv(filepath2, header = TRUE,sep = "\t",check.names = FALSE,quote = "\"")
pheno<-input_p#[,-1]
print("line")
print(pheno)

v=list()
v$data_wgcna<-data
v$pheno_wgcna<-get_pheno(v$data_wgcna,pheno)