plotFeatures: Plot features (cells or regions) based on dimensionality...

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

Plot features (cells or regions) based on dimensionality reduction over cell-topic or topic-region distributions

Description

Plot features (cells or regions) based on dimensionality reduction over cell-topic or topic-region distributions

Usage

plotFeatures(
  object,
  target,
  method = "tSNE",
  colorBy = NULL,
  dim = 2,
  intervals = 10,
  topic_contr = NULL,
  topics = NULL,
  col.low = "pink",
  col.mid = "red",
  col.high = "darkred",
  labels = 3,
  colVars = list(),
  plot_ly = FALSE,
  legend = TRUE,
  cex.legend = 0.7,
  factor.min = 0.05,
  factor.max = 0.75,
  cex.dot = 1,
  ...
)

Arguments

object	Initialized cisTopic object, after the object@dr has been filled.
target	Whether dimensionality reduction should be applied on cells ('cell') or regions (region). Note that for speed and clarity reasons, dimesionality reduction on regions will only be done using the regions assigned to topics with high confidence (see binarizecisTopics()).
method	Select the dimensionality reduction method to use for plotting: 'tSNE', 'Umap', 'PCA', 'Biplot', 'DM' (for Diffusion Map).
colorBy	Select the cell metadata used to colour the plots with. By default, all features are used.
dim	Dimensions to use in the plot (2 or 3). Biplot is only doable in 2D.
intervals	Intervals to apply on the color palette for coloring continuous variables. By default, it is 10.
topic_contr	Color by topic distribution ('Z-score' or 'Probability').
topics	Vector containing the numbers of the topics for which the plot has to be made if topic_contr is not null.
col.low	Color to use for lowest topic enrichment
col.mid	Color to use for medium topic enrichment
col.high	Color to use for high topic enrichment
labels	Labels for the Z-score in the continuous variables plots
plot_ly	Whether plot_ly should be used for the plots
legend	Whether plots should be given with a legend. If FALSE, the legend is given in an independent following plot.
cex.legend	Size of the legend
cex.dot	Size of the dot
...	Ignored.
colsVar	List specifying the colors to use for each label in each colouring level for cell metadata

Value

Plots cell states based on the dimensionality reduction method selected, coloured by the given metadata (one plot per feature).

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.