plot_grouped_geneset: Plot geneset scores as summary plot

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

Geneset scores are a score calculated for each single cell derived from \ more than one gene. This function plots geneset scores grouped with a boxplot overlaying a violin\ overlaying a jitter of the raw data.

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_grouped_geneset(
  cds,
  marker_set,
  name,
  by,
  fData_col = "gene_short_name",
  scale = "width",
  facet = NULL,
  adjust = 1.4,
  size = 0.05,
  alpha = 0.1,
  method = "totals",
  overlay_violinandbox = T,
  box_width = 0.3,
  rotate_x = T,
  jitter = T,
  return_values = F
)

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'
method	'totals' or 'corrected'. See estimate_score and estimate_corrected_score for more information

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/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.