plot_umap: Plot a UMAP data.frame

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Plot a UMAP data.frame

Usage

plot_umap(
  result,
  point_size = 0.7,
  no_legend = FALSE,
  label_clusters = TRUE,
  label_size = 3,
  legend_size = 3,
  text_box = TRUE,
  plotly = FALSE
)

Arguments

result	Result object containing UMAP data.frame
point_size	Scatter plot point size
no_legend	Remove legend
label_clusters	Add annotation labels to clusters (may not work well for split or small clusters)
label_size	Size of cluster labels
legend_size	Set legend size
text_box	Place a box around cluster labels for improved readability
plotly	Create plotly version of plot

Value

Returns a ggplot2 plot of the created umap, if plotly = TRUE the ggplotly object is returned

Examples

result <- readRDS(system.file("testdata", "res_annot.rds",
package = "BAGEL"))
create_umap(result, "Tumor_Subtypes", n_neighbors = 5)
plot_umap(result)

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.