visualiseDim

Source: R/clustering.R

A function to visualise the reduced dimension

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)
#> Calculating affinity matrix 
#> Performing SNF  
sce_control_subset <- reducedDimSNF(sce_control_subset,
method = "tSNE",
dimNames = "tSNE_joint")
visualiseDim(sce_control_subset, dimNames = "tSNE_joint",
colour_by = "SNF_W_clust")