DrawCluster: Drawing the cluster graph with "tsne" or "umap".

In bm2-lab/scLearn: Learning for single cell assignment

Drawing the cluster graph with "tsne" or "umap".

Usage

DrawCluster(data, label = NULL, point_size = 1, method = c("tsne", "umap"), draw_cluster_text = TRUE, calculated = TRUE, pca = TRUE, perplexity = 100, plot = TRUE, seed = 1)

Arguments

data	A matrix with column is sample, row is feature.
label	A vector showing the sample label corresponding the colnames of the matrix "data".
point_size	The size of point. Default is 1.
method	The method to plot which should be one of "tsne" and "umap". Default is "tsne".
draw_cluster_text	TRUE by default. If TRUE, the cluster label will be drawed in the corresponding place in the graph.
calculated	TRUE by default. If FALSE, "tsne" or "umap" will not be performed, the graph will be draw with data offered directly.
pca	TRUE by default. If FALSE, pca will not be performed.
perplexity	Default is 100.
plot	FALSE by default. If TRUE, plot the graph.
seed	Default is 1.

Value

p	The ggplot object for plotting.
x	A matrix showing coordinates calculated by "tsne" or "umap".
cell_group	A vector showing the cell label.

Author(s)

Bin Duan

bm2-lab/scLearn documentation built on Dec. 17, 2024, 8:18 p.m.