visualiseExprs: visualiseExprs

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

visualiseExprs

Description

A function to visualise the features distribtuion

Usage

visualiseExprs(
  sce,
  plot = c("boxplot", "violin", "jitter", "density", "pairwise"),
  altExp_name = c("none"),
  exprs_value = "logcounts",
  group_by = NULL,
  facet_by = NULL,
  feature_subset = NULL,
  cell_subset = NULL,
  n = NULL,
  threshold = NULL
)

Arguments

sce	A singlecellexperiment object
plot	Type of plot, includes boxplot, violin, jitter, density, and pairwise. By default is boxplot
altExp_name	A character indicates which expression matrix is used. by default is none (i.e. RNA).
exprs_value	A character indicates which expression value in assayNames is used.
group_by	A character indicates how is the expression will be group in the plots (stored in colData).
facet_by	A character indicates how is the expression will be lay out panels in a grid in the plots (stored in colData).
feature_subset	A vector of characters indicates the subset of features that are used for visualisation
cell_subset	A vector of characters indicates the subset of cells that are used for visualisation
n	A numeric indicates the top expressed features to show.
threshold	Thresholds of high expresion for features (only is used for pairwise plot).

Value

A ggplot to visualise te features distribution

Examples

data(sce_control_subset)
visualiseExprs(sce_control_subset,
plot = "boxplot",
group_by = "SNF_W_louvain",
feature_subset = c("hg19_CD8A"))

visualiseExprs(sce_control_subset,
plot = "density",
altExp_name = "ADT",
group_by = "SNF_W_louvain",
feature_subset = c("CD8", "CD4"))

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.