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Plot UMAP dimensionality reduction on DE genes

Source: R/plot_de_umap.R
plot_de_umap.Rd

Plot UMAP dimensionality reduction on DE genes

Usage

plot_de_umap(data = NULL, color_by = NULL, label = NULL, max_overlaps = NULL)

Arguments

data

A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column"

color_by

A string specifying which column in data will be used to color the samples.

label

A string specifying which column in data will be used to label a sample.

max_overlaps

Maximum number of overlaps for ggrepel

Value

ggplot object

Examples

if (FALSE) { # \dontrun{
data(mini_mac)
mini_mac_agg <- aggregate_by_de(mini_mac)
mini_mac_agg <- compute_de_umap(mini_mac_agg)
mini_mac_agg <- Seurat::FindNeighbors(mini_mac_agg, reduction = "umap_de", dims = 1:2, verbose = FALSE)
mini_mac_agg <- Seurat::FindClusters(mini_mac_agg, resolution = 1, verbose = FALSE)
mini_mac_agg <- compute_de_umap(mini_mac_agg)
p <- plot_de_umap(mini_mac_agg)
} # }