visualiseExprs {CiteFuse} | R Documentation

## visualiseExprs

### Description

A function to visualise the features distribtuion

### Usage

    visualiseExprs(
      sce,
      plot = c("boxplot", "violin", "jitter", "density", "pairwise"),
      altExp_name = c("none"),
      exprs_value = "logcounts",
      group_by = NULL,
      facet_by = NULL,
      feature_subset = NULL,
      cell_subset = NULL,
      n = NULL,
      threshold = NULL
    )

### Arguments

`sce` | A 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).
`facet_by` | A character indicates how is the expression will be lay out panels in a grid 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.
`threshold` | Thresholds of high expresion for features (only is used for pairwise plot).

### Value

A ggplot to visualise te features distribution

### Examples

    data(sce_control_subset)
    visualiseExprs(sce_control_subset,
    plot = "boxplot",
    group_by = "SNF_W_louvain",
    feature_subset = c("hg19_CD8A"))

    visualiseExprs(sce_control_subset,
    plot = "density",
    altExp_name = "ADT",
    group_by = "SNF_W_louvain",
    feature_subset = c("CD8", "CD4"))

[Package CiteFuse version 1.2.1 Index]