minor correction in report

wbaopaul · Oct 29, 2020 · 78f0980 · 78f0980
1 parent e69266d
commit 78f0980
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/scripts/src/clustering.R b/scripts/src/clustering.R
@@ -83,6 +83,7 @@ if(cluster_method == 'seurat'){
   seurat.obj$active_clusters = seurat.obj$seurat_clusters
 }
 
+k = as.integer(k)
 
 if(grepl(REDUCTION, pattern = 'lda', ignore.case = T)){
 

diff --git a/scripts/src/scATAC-pro_report.Rmd b/scripts/src/scATAC-pro_report.Rmd
@@ -98,7 +98,7 @@ lib_complx = paste0(100 * round(lib_complx, 3), '%')
 mapping_qc$frac = round(mapping_qc$V2/mapping_qc$V2[1], 3)
 mapping_qc$frac = paste0(100*mapping_qc$frac, '%')
 
-mapping_qc = rbind(mapping_qc, data.frame(V1 ='Library Complexity (nonredudant fraction)', V2 = '', frac = lib_complx))
+mapping_qc = rbind(mapping_qc, data.frame(V1 ='Library Complexity (#unique fragments/#fragments)', V2 = '', frac = lib_complx))
 
 kable(mapping_qc, col.names = NULL, format = 'html', caption = paste('Sample:', OUTPUT_PREFIX)) %>%
   kable_styling("striped", full_width = F, position = 'left', font_size = 15)
@@ -187,12 +187,12 @@ if(CELL_MAP_QC){
     cell_mapping_qc$frac = round(cell_mapping_qc$V2/cell_mapping_qc$V2[1], 3)
     cell_mapping_qc$frac = paste0(100*cell_mapping_qc$frac, '%')
 
-    cell_mapping_qc = rbind(cell_mapping_qc, data.frame(V1 ='Library Complexity (nonredudant fraction)', V2 = '', frac = lib_complx))
+    cell_mapping_qc = rbind(cell_mapping_qc, data.frame(V1 ='Library Complexity (#unique fragments/#fragments)', V2 = '', frac = lib_complx))
 
     write.table(cell_mapping_qc, file = paste0(params$output_dir, '/summary/Tables/Cell_Mapping_QC.tsv'),
 		col.names = F, quote = F, row.names = F, sep = '\t')
 
-    kable(cell_mapping_qc, row.names = T, col.names = NULL, format = 'html') %>%
+    kable(cell_mapping_qc, row.names = F, col.names = NULL, format = 'html') %>%
       kable_styling("striped", full_width = F, position = 'left', font_size = 15)
-Original file line number
+Diff line change
@@ Expand Up / @@ -83,6 +83,7 @@ if(cluster_method == 'seurat'){ @@
       seurat.obj$active_clusters = seurat.obj$seurat_clusters
     }
+    k = as.integer(k)
     if(grepl(REDUCTION, pattern = 'lda', ignore.case = T)){
@@ Expand Down @@