plotFeature: Plot Feature

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Plot Feature

Usage

plotFeatureTSNE(object, ...)

plotFeatureUMAP(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotFeatureTSNE(object, features,
  color = NULL, pointSize = getOption("pointSize", 0.75),
  pointAlpha = getOption("pointAlpha", 0.75), label = TRUE,
  labelSize = getOption("labelSize", 6L), dark = FALSE, grid = FALSE,
  legend = FALSE, aspectRatio = 1L)

## S4 method for signature 'seurat'
plotFeatureTSNE(object, features, color = NULL,
  pointSize = getOption("pointSize", 0.75),
  pointAlpha = getOption("pointAlpha", 0.75), label = TRUE,
  labelSize = getOption("labelSize", 6L), dark = FALSE, grid = FALSE,
  legend = FALSE, aspectRatio = 1L)

## S4 method for signature 'SingleCellExperiment'
plotFeatureUMAP(object, features,
  color = NULL, pointSize = getOption("pointSize", 0.75),
  pointAlpha = getOption("pointAlpha", 0.75), label = TRUE,
  labelSize = getOption("labelSize", 6L), dark = FALSE, grid = FALSE,
  legend = FALSE, aspectRatio = 1L)

## S4 method for signature 'seurat'
plotFeatureUMAP(object, features, color = NULL,
  pointSize = getOption("pointSize", 0.75),
  pointAlpha = getOption("pointAlpha", 0.75), label = TRUE,
  labelSize = getOption("labelSize", 6L), dark = FALSE, grid = FALSE,
  legend = FALSE, aspectRatio = 1L)

Arguments

object	Object.
...	Additional arguments.
features	Character vector of features (e.g. gene expression, PC scores, number of genes detected).
color	Desired ggplot color scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().
pointSize	Cell point size.
pointAlpha	Alpha transparency level. Useful when there many cells in the dataset, and some cells can be masked.
label	Overlay a cluster identitiy label on the plot.
labelSize	Size of the text label.
dark	Plot against a dark background using basejump::theme_midnight().
grid	Show major grid lines but hide axis lines.
legend	Include plot legend.
aspectRatio	Aspect ratio.

Value

ggplot or list.

Author(s)

Michael Steinbaugh

See Also

Seurat::FeaturePlot().

Other Clustering Functions: cellTypesPerCluster, knownMarkersDetected, plotCellTypesPerCluster, plotKnownMarkersDetected, plotPCElbow, plotTSNE, sanitizeMarkers, topMarkers

Examples

# seurat ====
object <- seurat_small
features <- c("nUMI", "nGene", "PC1", "PC2")

# t-SNE
plotFeatureTSNE(object, features)

# UMAP
plotFeatureUMAP(object, features)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.