plotBambu {bambu} | R Documentation

## plot.bambu

### Description

plotSEOuptut

### Usage

    plotBambu(
        se,
        group.variable = NULL,
        type = c("annotation", "pca", "heatmap"),
        gene_id = NULL,
        transcript_id = NULL
    )

### Arguments

`se` | An summarized experiment object obtained from `bambu` or `transcriptToGeneExpression`.
`group.variable` | Variable for grouping in plot, has be to provided if choosing to plot PCA.
`type` | plot type variable, a values of annotation for a single gene with heatmap for isoform expressions, pca, or heatmap, see details.
`gene_id` | specifying the gene_id for plotting gene annotation, either gene_id or transcript_id has to be provided when type = "annotation".
`transcript_id` | specifying the transcript_id for plotting transcript annotation, either gene_id or transcript_id has to be provided when type = "annotation"

### Details

`type` indicates the type of plots to be plotted. There are two types of plots can be chosen, PCA or heatmap.

### Value

A heatmap plot for all samples

### Examples

    se <- readRDS(system.file("extdata",
    "seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
    package = "bambu"))
    plotBambu(se, type = "PCA")

[Package bambu version 1.2.1 Index]