gene_count_hist: This function returns a histogram of the number of spots that...

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 a histogram of the number of spots that detected a gene.

Description

This function returns a histogram of the number of spots that detected a gene.

Usage

gene_count_hist(
  se,
  slot = "counts",
  assay = "Spatial",
  sample_id = "orig.ident"
)

Arguments

se	Spatial Seurat object we want to assess.
slot	slot from where we want to extract the count matrix.
assay	assay from where we want to extract the count matrix.
sample_id	Feature in metadata by which to identify the sample if the object is merged and contains several samples.

Value

List with the 4 QC plots

Examples

## Not run: 
library(Seurat)
library(SeuratData)
sp_obj <- SeuratData::LoadData(ds = "stxBrain", type = "posterior1")
gene_count_hist(
  se = sp_obj,
  slot = "counts",
  assay = "Spatial",
  sample_id = "orig.ident")

## End(Not run)

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