plotExp: Plot expression of genes

In powellgenomicslab/scExplore: Single-cell Data Visualization

Description

This function allows to plot the expression of genes in individual color scales and their corresponding "merge" visualization

Usage

plotExp(object, gene1, gene2 = NULL, dims = c(1, 2),
  reduction = "umap", group = NULL, subset = NULL, type = "data",
  qclip = 1, dropout = FALSE, alpha = 0.7, size = 0.3,
  bgColor = "gray20", returnGrid = TRUE)

Arguments

object	A Seurat object
gene1	Gene 1
gene2	Gene 2 (optional)
dims	Dimensions to plot. Only two are valid.
reduction	Dimensionality reduction (e.g. pca, umap, tsne, ...)
group	Group variable in metadata
type	Data type: counts or data slots
qclip	Quantile value to clip gene expression values. This parameter reduces the effect of outlier cells with high gene expression according to a quantile of the distribution (default 1: No clipping). All cells for each gene expressing a value greater to the quantile value in the distribution are rescaled to the corresponding value of that quantile
dropout	Binarizes gene expression data. Assigns 1 to gene expression values greater than 0
alpha	Alpha level to adjust transparency of colors
size	Size of points
bgColor	Background color
returnGrid	If TRUE, a grid is generated using cowplot. Otherwise, a list with the plots is returned

Value

A grid plot with individual genes and merge gene expression values

Author(s)

José Alquicira Hernández

Examples

# Plot gene expression of CD8A and CD3D from log-normalized data over a UMAP plot

plotMerge(pbmc, "CD8A", "CD3D", reduction = "umap", type = "data")

powellgenomicslab/scExplore documentation built on Nov. 5, 2019, 1:12 a.m.