QC.violinPlot: QC violin plots

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

QC violin plots

Description

Number of genes/cell, UMI/cell and mitochondiral content/cell are visualized with violin plots. Two ggplot handles are generated. First contains QC metrics pooled across all cells, while second stratifies dataset by grouping variable.

Usage

QC.violinPlot(
  so,
  features = c("nFeature_RNA", "nCount_RNA", "percent.mt"),
  group.by = NULL,
  plt.log.flag = T,
  ...
)

Arguments

so	Seurat Object
features	meta data features to plot. Default is c("nFeature_RNA", "nCount_RNA", "percent.mt").
group.by	meta data field to group plots by.
plt.log.flag	Logical specifying whether data are plotted on log scale. Default is True.
...	additional arguments passed to Seurat::VlnPlot(...)

Value

list of ggplot handles

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.