FilterQC test functions

Author: phoman14

NAMESPACE

@@ -48,14 +48,19 @@ import(scales)
 import(tidyverse)
 import(tools)
 import(utils)
+importFrom(BiocParallel,SerialParam)
 importFrom(ComplexHeatmap,pheatmap)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RColorBrewer,brewer.pal.info)
 importFrom(Seurat,AddMetaData)
 importFrom(Seurat,CreateAssayObject)
 importFrom(Seurat,DotPlot)
+importFrom(Seurat,FindVariableFeatures)
 importFrom(Seurat,Idents)
+importFrom(Seurat,RunPCA)
 importFrom(Seurat,RunTSNE)
+importFrom(Seurat,RunUMAP)
+importFrom(Seurat,SCTransform)
 importFrom(Seurat,as.SingleCellExperiment)
 importFrom(SingleR,SingleR)
 importFrom(colorspace,RGB)
@@ -75,6 +80,7 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,pull)
 importFrom(dplyr,relocate)
+importFrom(dplyr,rename)
 importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
@@ -97,8 +103,13 @@ importFrom(ggpubr,annotate_figure)
 importFrom(ggpubr,get_legend)
 importFrom(ggpubr,ggarrange)
 importFrom(grDevices,colorRampPalette)
+importFrom(grid,gTree)
 importFrom(grid,grid.draw)
+importFrom(grid,grid.newpage)
+importFrom(grid,grobHeight)
+importFrom(grid,textGrob)
 importFrom(gridExtra,arrangeGrob)
+importFrom(gridExtra,tableGrob)
 importFrom(htmlwidgets,saveWidget)
 importFrom(magrittr,"%>%")
 importFrom(plotly,as_widget)
@@ -110,9 +121,12 @@ importFrom(scales,rescale)
 importFrom(stats,as.hclust)
 importFrom(stats,hclust)
 importFrom(stats,kmeans)
+importFrom(stats,mad)
+importFrom(stats,median)
 importFrom(stats,quantile)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sort)
+importFrom(stringr,str_split_fixed)
 importFrom(stringr,str_to_title)
 importFrom(stringr,str_wrap)
 importFrom(tibble,deframe)

R/Filter_QC.R

@@ -91,6 +91,8 @@
 #' @importFrom Seurat CreateAssayObject Idents as.SingleCellExperiment 
 #' @importFrom Seurat AddMetaData SCTransform FindVariableFeatures
 #' @importFrom Seurat RunPCA RunUMAP
+#' @importFrom BiocParallel SerialParam
+#' @importFrom stringr str_split_fixed 
 #' @importFrom reshape2 melt
 #' @importFrom magrittr %>%
 #' @importFrom dplyr arrange rename