visualiseDim: visualiseDim

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

Description

A function to visualise the reduced dimension

Usage

visualiseDim(
  sce,
  dimNames = NULL,
  colour_by = NULL,
  shape_by = NULL,
  data_from = c("colData", "assay", "altExp"),
  assay_name = NULL,
  altExp_name = NULL,
  altExp_assay_name = NULL,
  dim = seq_len(2)
)

Arguments

sce	A singlecellexperiment object
dimNames	indicates the name of the reduced dimension results.
colour_by	A character indicates how the cells coloured by. The information either stored in colData, assay, or altExp.
shape_by	A character indicates how the cells shaped by. The information either stored in colData, assay, or altExp.
data_from	A character indicates where the colour by data stored
assay_name	A character indicates the assay name of the expression
altExp_name	A character indicates the name of alternative expression
altExp_assay_name	A character indicates the assay name of alternative expression
dim	a vector of numeric with length of 2 indicates which component is being plot

Value

A ggplot of the reduced dimension visualisation

Examples

data(sce_control_subset, package = "CiteFuse")
sce_control_subset <- CiteFuse(sce_control_subset)
sce_control_subset <- reducedDimSNF(sce_control_subset,
method = "tSNE",
dimNames = "tSNE_joint")
visualiseDim(sce_control_subset, dimNames = "tSNE_joint",
colour_by = "SNF_W_clust")

CiteFuse documentation built on April 14, 2021, 6 p.m.