Description Usage Arguments Examples
Visualize normalized expression of selected genes on tSNE plot with color-code and contour annotation.
1 2 | plot_contour_overlay_tSNE(environment, genes, perplexity = 30,
max_iter = 10000, width = 10, height = 10)
|
environment |
|
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 |
1 2 3 4 5 6 | 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'))
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