plot_contour_overlay_tSNE: Plot Gene Expression on tSNE

In asmagen/robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

Plot Gene Expression on tSNE

Description

Visualize normalized expression of selected genes on tSNE plot with color-code and contour annotation.

Usage

plot_contour_overlay_tSNE(environment, genes, perplexity = 30,
  max_iter = 10000, width = 10, height = 10)

Arguments

environment	environment object
genes	selected genes to visualize
perplexity	tSNE perplexity parameter
max_iter	tSNE max_iter parameter
width	pdf file canvas width
height	pdf file canvas height

Examples

LCMV1 <- setup_LCMV_example()
LCMV1 <- get.variable.genes(LCMV1, min.mean = 0.1, min.frac.cells = 0,
min.dispersion.scaled = 0.1)
LCMV1 <- PCA(LCMV1)
LCMV1 <- cluster.analysis(LCMV1)
plot_contour_overlay_tSNE(LCMV1,genes = c('Cd4','Cd8a'))

asmagen/robustSingleCell documentation built on July 30, 2023, 6:48 a.m.