plotFeature: Plot specific feature on t-SNE coordinates

In rliger: Linked Inference of Genomic Experimental Relationships

Plot specific feature on t-SNE coordinates

Description

Generates one plot for each dataset, colored by chosen feature (column) from cell.data slot. Feature can be categorical (factor) or continuous. Can also plot all datasets combined with by.dataset = FALSE.

Usage

plotFeature(
  object,
  feature,
  by.dataset = TRUE,
  discrete = NULL,
  title = NULL,
  pt.size = 0.3,
  text.size = 3,
  do.shuffle = TRUE,
  rand.seed = 1,
  do.labels = FALSE,
  axis.labels = NULL,
  do.legend = TRUE,
  legend.size = 5,
  option = "plasma",
  cols.use = NULL,
  zero.color = "#F5F5F5",
  return.plots = FALSE
)

Arguments

object	liger object. Should call runTSNE or runUMAP before calling.
feature	Feature to plot (should be column from cell.data slot).
by.dataset	Whether to generate separate plot for each dataset (default TRUE).
discrete	Whether to treat feature as discrete; if left NULL will infer from column class in cell.data (if factor, treated like discrete) (default NULL).
title	Plot title (default NULL).
pt.size	Controls size of points representing cells (default 0.3).
text.size	Controls size of plot text (cluster center labels) (default 3).
do.shuffle	Randomly shuffle points so that points from same dataset are not plotted one after the other (default TRUE).
rand.seed	Random seed for reproducibility of point shuffling (default 1).
do.labels	Print centroid labels for categorical features (default FALSE).
axis.labels	Vector of two strings to use as x and y labels respectively.
do.legend	Display legend on plots (default TRUE).
legend.size	Size of legend spots for discrete data (default 5).
option	Colormap option to use for ggplot2's scale_color_viridis (default 'plasma').
cols.use	Vector of colors to form gradient over instead of viridis colormap (low to high). Only applies to continuous features (default NULL).
zero.color	Color to use for zero values (no expression) (default '#F5F5F5').
return.plots	Return ggplot plot objects instead of printing directly (default FALSE).

Value

List of ggplot plot objects (only if return.plots TRUE, otherwise prints plots to console).

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iter = 1)
ligerex <- quantile_norm(ligerex)
ligerex <- runTSNE(ligerex)
plotFeature(ligerex, "nUMI", pt.size = 1)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.