% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/clustering.R
 \name{visualiseDim}
 \alias{visualiseDim}

 \title{visualiseDim}

 \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{
 \item{sce}{A singlecellexperiment object}
 
 \item{dimNames}{indicates the name of the reduced dimension results.}
 

 \item{colour_by}{A character indicates how the cells coloured by.
 The information either stored in colData, assay, or altExp.}

 \item{shape_by}{A character indicates how the cells shaped by.
 The information either stored in colData, assay, or altExp.}
 
 \item{data_from}{A character indicates where the colour by data stored}
 
 \item{assay_name}{A character indicates the assay name of the expression}
 
 \item{altExp_name}{A character indicates the name of alternative expression}
 

 \item{altExp_assay_name}{A character indicates the assay name
 of alternative expression}

 \item{dim}{a vector of numeric with length of 2 indicates
 which component is being plot}

 }

 \value{
 A ggplot of the reduced dimension visualisation
 }

 \description{
 A function to visualise the reduced dimension
 }

 \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")
 
 }