From 78f0980379addf1abcb5898f99b3d958ff6d3920 Mon Sep 17 00:00:00 2001 From: wbaopaul Date: Thu, 29 Oct 2020 10:37:11 -0400 Subject: [PATCH] minor correction in report --- scripts/src/clustering.R | 1 + scripts/src/scATAC-pro_report.Rmd | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/scripts/src/clustering.R b/scripts/src/clustering.R index 7f339c6..47100af 100644 --- 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 index e7e3583..8742c08 100644 --- 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)