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I'm trying to run pvclust as a test Im running it in small subset of files. The issue is it works but instead of list which i would have used downstream to print it to individual files it gets printed.

My code

list_of_files <- list.files('Model_pvclust/',pattern = '\\.txt$', full.names = TRUE)


cmplx_ht<-function(file_list){
  start_time <- Sys.time()
  df_list<-list()
  #heat_list<-list()
  pv_list<-list()
  require(pvclust)
  
  for(f in file_list){
    message(paste0("Making pvclust for: ",f))
    
    #fname <- gsub("Model_hmap\/\/|\.txt","",f)
    df <- read.csv(f, header = TRUE, sep = "\t", check.names = FALSE)
    mat <- t(scale(t(as.matrix(df[,grepl("TCGA-",colnames(df))]))))
    rownames(mat)<-df$Symbol
    df_list[[f]]<-mat
    #print(head(mat))
   hm <-  pvclust(as.data.frame(t(mat)), method.hclust="complete",
            method.dist="euclidian",nboot = 10, parallel=T)
    
    #heat_list[[f]]<-hm 
    plot(hm)
   b <-pvrect(hm, alpha=.95)
   pv_list[[f]] <-b 
   #dev.off()
   
  # dev.off()
    message("Done")
  }
  end_time <- Sys.time()
  time_taken<- end_time-start_time
  message(paste0(time_taken,"s"))
  return(pv_list)
}

hm_lst<-cmplx_ht(list_of_files)

To print it to individual files this is what Im doing

for (i in 1:length(hm_lst)) {
  file_name = paste(names(hm_lst)[[i]],".pdf", sep="")
  #file_name = paste(names(hm_lst),".pdf", sep="")
  
  pdf(file_name,width = 15,height = 10)
  draw(hm_lst[[i]])
  dev.off()
}

But my hm_list is coming empty the output is getting printed which i don't want. I want to store the output as lists the want to print it to files

Im not sure what exactly I'm doing wrong. Any suggestion or help would be really appreciated

PesKchan
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1 Answers1

3

You can use recordPlot to store a base plot in a object.

x = 1:10

plot(x)

# record the plot
g <- recordPlot()

# clean the device
plot.new()

# plot is saved to g
g

plot in object g

shafee
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  • what is the issue with my code here? – PesKchan Jul 09 '22 at 16:32
  • 1
    From your code what I understand is that you are trying to assign the plot in `pv_list`, but in R, you can assign function output to a variable if that function returns anything, but `plot` function returns `NULL`. That's why your `pv_list` and eventually `hm_list` is just empty (i.e. `NULL`) – shafee Jul 09 '22 at 16:57
  • okay now it worked as I used your ''g <- recordPlot()' this one – PesKchan Jul 09 '22 at 17:22