visualiseDim {CiteFuse} | R Documentation

## visualiseDim

### 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")

[Package CiteFuse version 1.2.1 Index]