plotFeature: Plot Feature

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot Feature

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
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

1
2
3
4
5
6
7
8
9
# seurat ====
object <- seurat_small
features <- c("nUMI", "nGene", "PC1", "PC2")

# t-SNE
plotFeatureTSNE(object, features)

# UMAP
plotFeatureUMAP(object, features)

WeiSong-bio/roryk-bcbioSinglecell documentation built on July 6, 2019, 12:03 a.m.