expression.Plot: Violin plot of single cell gene expression

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

Violin plot of single cell gene expression

Description

Draws violin plot of single cell data, stratified by specified group. Hierarchically-clustered dendrogram is overlaid to illustrate relationships between groups.

Usage

expression.Plot(
  so,
  which.gene,
  e.mat = NULL,
  f.mat = NULL,
  which.group = "seurat_clusters",
  which.data = "data",
  which.assay = DefaultAssay(so),
  x.label = NULL,
  x.label.angle = NULL,
  show.violin = T,
  show.full.axis = T,
  font.size = NULL,
  verbose = T
)

Arguments

so	Seurat object
which.gene	query gene. Must be available in Seurat object.
e.mat	expression matrix (gene x cell). If not provided, computed from seurat object (more computationally heavy).
f.mat	expression fraction matrix (gene x cell). If not provided, computed from seurat object (more computationally heavy).
which.group	Group to cluster gene expression by. Must be column header in so meta data. Default is "seurat_clusters".
which.data	Specifies which seurat data used to compute e.mat and f.mat. Must be either "data" (default) or "scale". Used only if e.mat and f.mat are not provided.
which.assay	Specifies which seurat assay to used to compute e.mat. Used only if e.mat is not provided. Default is DefaultAssay(so)
x.label	x axis title (a character). Default is which.group.
x.label.angle	rotation angle for x axis title (a numeric). Default is NULL.
show.violin	Show expression as violin plot. Default is T.
show.full.axis	Show full normalized axis [0,1], rather than adapting to data. Default is T.
font.size	Size of font.
verbose	print progress. Default is T.

Value

ggplot object

Examples

# get expression plot of GPNMB stratified by cluster group.
plt.sgExp.clust <- expression.Plot.dev(so.query, which.gene = "GPNMB", which.group = "seurat_clusters", which.data = "data")
print(plt.sgExp.clust)

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