Plot Sample PCA (Deprecated)

This function is deprecated. Please use plotSampleEmbedding with .embedding = "pca" instead.

Usage

plotSamplePCA(x, ...)

# S3 method for class 'TDRObj'
plotSamplePCA(
  x,
  .labels.from = colnames(x = .tdr.obj@metadata)[1],
  .cat.feature.color = Color.Palette[1, 1:5],
  .point.size = 1,
  .panel.size = 2,
  .midpoint = if (is.numeric(x = .tdr.obj@metadata[[.labels.from]])) stats::median(x =
    .tdr.obj@metadata[[.labels.from]]) else NA,
  ...
)

Arguments

x

A TDRObj, Seurat, SingleCellExperiment, or HDF5AnnData (anndataR) object processed through get.map() and get.embedding().

...

Additional arguments passed to methods.

.labels.from

Character specifying metadata column for coloring points.

.cat.feature.color

Character vector of colors for categorical labels.

.point.size

Numeric point size (default 1).

.panel.size

Numeric panel width/height in inches (default 2).

.midpoint

Numeric midpoint for diverging color scale (continuous labels only).

Value

A ggplot object showing PC1 vs PC2 of sample-level density profiles.

See also

plotSampleEmbedding for the recommended replacement