qc_st_plots: This function returns QC metric plots with Spatial Seurat...

In Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package: R package to store useful functions to analyze single-cell data that the entire team can benefit

This function returns QC metric plots with Spatial Seurat objects.

Description

This function returns QC metric plots with Spatial Seurat objects.

Usage

qc_st_plots(
  se,
  nfeat = "nFeature_Spatial",
  ncount = "nCount_Spatial",
  slot = "counts",
  assay = "Spatial",
  percent.mito = NULL,
  percent.ribo = NULL
)

Arguments

se	Spatial Seurat object we want to assess.
nfeat	Character string indicating the name of the variable in the metadata containing the number of genes.
ncount	Character string indicating the name of the variable in the metadata containing the number of UMIs.
slot	slot from where we want to extract the count matrix.
assay	assay from where we want to extract the count matrix.
percent.mito	Character string indicating the name of the variable in the metadata containing the mitochondrial percentage. Defaults to NULL in which case it computes it using the gollowing regex "^MT-".
percent.ribo	Character string indicating the name of the variable in the metadata containing the ribosomal percentage. Defaults to NULL in which case it computes it using the gollowing regex "^RPL|^RPS".

Value

List with the 4 QC plots

Examples

## Not run: 
library(Seurat)
library(SeuratData)
sp_obj <- SeuratData::LoadData(ds = "stxBrain", type = "posterior1")
qc_st_plots(
  se = sp_obj,
  nfeat = "nFeature_Spatial",
  ncount = "nCount_Spatial",
  slot = "counts",
  assay = "Spatial") %>%
cowplot::plot_grid(
  plotlist = .,
  align = "hv",
  axis = "trbl")

## End(Not run)

Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package documentation built on Aug. 20, 2022, 9:29 a.m.