plotBambu: plot.bambu

In bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

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")

bambu documentation built on Nov. 12, 2020, 2:01 a.m.