rliger (version 1.0.1)

plotFeature: 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
)

Value

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

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).

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)