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Plot results of UMAP

Source: R/plot-umap.R
plot_umap.Rd

This function creates a simple plot of the data.frame returned by the umap() function.

Usage

plot_umap(
  df,
  x = "UMAP1",
  y = "UMAP2",
  colBy = NULL,
  shapeBy = NULL,
  pointSize = 3,
  pointAlpha = 1,
  hline = 0,
  vline = 0,
  hlineType = 2,
  vlineType = 2
)

Arguments

df

data.frame of UMAP embeddings and metadata

x

First UMAP component. Default "UMAP1"

y

Second UMAP component. Default "UMAP2"

colBy

Column name of data.frame to color points by. Default NULL

shapeBy

Column name of data.frame to shape the points by. Default NULL

pointSize

Size of the points. Default 3

pointAlpha

Alpha level of the points. Default 1

hline

y-position of horizontal line. Default 0

vline

x-position of vertical line. Default 0

hlineType

linetype of the horizontal line. Default 2

vlineType

linetype of the vertical line. Default 2

Value

ggplot object

Examples

# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# PCA with PCAtools
p <- PCAtools::pca(GSE161650_lc, metadata, center = TRUE, scale = TRUE)
udata <- coriell::UMAP(p, n_neighbors = 2)
#> Warning: failed creating initial embedding; using random embedding instead
#> Warning: failed creating initial embedding; using random embedding instead
plot_umap(udata, colBy = "Group")