plotDimDiscretized: Dimensionality Reduction Plot (Multi-Color, Discretized)

In farrellja/URD: URD

Description

Plots cells according to their coordinates in a dimensionality reduction (tSNE by default). Cells are colored according to which of 1-3 labels are 'on' after conversion to discrete on/off values according to label.min and label.max. All labels must be continuous variables (i.e. not cluster identities).

Usage

plotDimDiscretized(
  object,
  labels,
  label.types = rep("search", length(labels)),
  label.min = rep(0, length(labels)),
  label.max = rep(Inf, length(labels)),
  colors = c("grey", "blue", "green", "red", "cyan", "magenta", "yellow", "black"),
  reduction.use = c("tsne", "pca", "dm"),
  dim.x = 1,
  dim.y = 2,
  point.size = 1,
  alpha = 1,
  plot.title = NULL,
  x.lim = NULL,
  y.lim = NULL
)

Arguments

object	An URD object
labels	(Character vector, length 1-3) Data to plot
label.types	(Character vector, length 1-3) Type of data to search for the label for the first channel. Default is "search" which checks several data types in order. For more information: data.for.plot
label.min	(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between label.min and label.max
label.max	(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between label.min and label.max
colors	(Character vector) Colors to use for plotting. Color order is as follows: With one label (A): 1 A-, 2 A+; With two labels (A, B): 1 A- B-, 2 A+ B-, 3 A- B+, 4 A+ B+; With three labels (A, B, C): 1 A- B- C-, 2 A+ B- C-, 3 A- B+ C-, 4 A- B- C+, 5 A+ B+ C-, 6 A+ B- C+, 7 A- B+ C+, 8 A+ B+ C+
reduction.use	(Character) Dimensionality reduction to use (tSNE, PCA, or Diffusion Map)
dim.x	(Numeric) Component to use on x-axis
dim.y	(Numeric) Component to use on y-axis
point.size	(Numeric) Size of points on plot
alpha	(Numeric) Transparency of points on plot: 0 (Transparent) - 1 (Opaque)
plot.title	(Character) Title of the plot
x.lim	(Numeric) Limits of x-axis (NULL autodetects)
y.lim	(Numeric) Limits of y-axis (NULL autodetects)

Details

Shamelessly inspired by the behavior of FeaturePlot in Seurat when overlay is turned on.

Value

A ggplot2 object

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.