visualiseExprsList: visualiseExprsList

View source: R/visualise_features.R

visualiseExprsListR Documentation

visualiseExprsList

Description

A function to visualise the features distribtuion for a list of SingleCellExperiment

Usage

visualiseExprsList(
  sce_list,
  plot = c("boxplot", "violin", "jitter", "density"),
  altExp_name = "none",
  exprs_value = "logcounts",
  group_by = NULL,
  feature_subset = NULL,
  cell_subset = NULL,
  n = NULL
)

Arguments

sce_list

A list of 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).

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.

Value

A ggplot to visualise te features distribution

Examples

data(sce_control_subset, package = "CiteFuse")
data(sce_ctcl_subset, package = "CiteFuse")
visualiseExprsList(sce_list = list(control = sce_control_subset,
ctcl = sce_ctcl_subset),
plot = "boxplot",
altExp_name = "none",
exprs_value = "logcounts",
feature_subset = c("hg19_CD8A"),
group_by = c("SNF_W_louvain", "SNF_W_louvain"))



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