plot_geneset: Plot geneset scores as cells

In scfurl/viewmaster: This package aims annotate scRNAseq data according to a reference

Plot geneset scores as cells

Description

Geneset scores are a score calculated for each single cell derived from \ more than one gene. This function plots geneset scores using monocle3's 'plot_genes' function.

When using method 'totals', the sum of the size-factor corrected, log-normalized gene \ expression for a give set of genes is performed. When using method 'corrected', single \ cell scores for a give gene set that have been "corrected" using 100X genes with similar \ expression levels.

Usage

plot_geneset(
  cds,
  marker_set,
  name,
  fData_col = "gene_short_name",
  method = c("totals", "corrected"),
  reduction_method = "UMAP",
  cell_size = 0.5
)

Arguments

cds	Input cell_data_set object.
marker_set	Vector of genes in the gene_metadata DataFrame (fData) that can be found in the column 'fData_col'
name	Name given to the geneset
fData_col	Character string denoting the gene_metadata DataFrame (fData) column that contains the genes in marker_set1. Default = 'gene_short_name'
cell_size	size of point on plot

Value

Plot

References

Puram, S. V. et al. Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell 171, 1611.e1–1611.e24 (2017).

scfurl/viewmaster documentation built on Nov. 22, 2022, 2:59 p.m.