plotFeature: Plot feature on low-dimensional space

In powellgenomicslab/scExplore: Single-cell Data Visualization

Description

This function allows to plot the values of a feature (gene or metadata column) on a low-dimensional space

Usage

plotFeature(object, feature, dims = c(1, 2), reduction = "umap",
  group = NULL, subset = NULL, type = "data", qclip = 1,
  label = TRUE, legend = TRUE, alpha = 0.7, size = 0.3,
  legPtSize = 4, pal = NULL)

Arguments

object	A Seurat object
feature	Feature to be plotted (gene expression or metadata)
dims	Dimensions to plot. Only two are valid.
reduction	Dimensionality reduction (e.g. pca, umap, tsne, ...)
group	Group variable in metadata
type	If gene expression is used, specify, rata type: counts or data slots
qclip	Quantile value to clip gene expression values or continuous variables. 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
label	Label clusters when a categorical variable is used
alpha	Alpha level to adjust transparency of colors
size	Size of points
pal	Color palette to use
label	Include legend?

Value

A plot with feature of interest

Author(s)

José Alquicira Hernández

Examples

# Plot clusters

plotFeature(pbmc, "seurat_clusters")

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