minor correction on report

wbaopaul · Jul 16, 2020 · 0ff2dbd · 0ff2dbd
1 parent 0e75c94
commit 0ff2dbd
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/scripts/runCicero.sh b/scripts/runCicero.sh
@@ -16,4 +16,4 @@ curr_dir=`dirname $0`
 
 ${R_PATH}/Rscript --vanilla ${curr_dir}/src/runCicero.R $seuratObj_file $output_dir $TSS $CHROM_SIZE_FILE
 
-echo "Differential analysis done!"
+echo "runCicero done!"
diff --git a/scripts/src/scATAC-pro_report.Rmd b/scripts/src/scATAC-pro_report.Rmd
@@ -391,14 +391,15 @@ if(file.exists(seurat_file)){
 go_file = paste0(down.dir, '/enrichedGO_differential_accessible_features_', group1, 
                   '_vs_', group2, '.xlsx')
 if(file.exists(go_file)){
-   #library(xlsx)
-    cls = 1:length(unique(ss$active_clusters))
     if(grepl(group1, pattern = 'one')){
       tmp = list()
-      for(i in 1:length(cls)) tmp[[i]] = xlsx::read.xlsx(go_file, i)
+      wb <- xlsx::loadWorkbook(go_file)
+      sheets = xlsx::getSheets(wb)
+      for(i in names(sheets)) tmp[[i]] = xlsx::read.xlsx(go_file, sheetName = i)
       ll = sapply(tmp, nrow)
       go_res = tmp[[which.max(ll)]]
-      group.sele = cls[which.max(ll)]
+      group.sele = names(sheets)[which.max(ll)]
+      group.sele = gsub('cluster', '', group.sele)
     }else{
        go_res1 = xlsx::read.xlsx(go_file, sheetName = paste0('cluster', group1))
        go_res2 = xlsx::read.xlsx(go_file, sheetName = paste0('cluster', group2))