visualiseExprsList: visualiseExprsList

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

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.