gettRNAFeaturePlots: Graphical summary of tRNA features

In FelixErnst/tRNA: Analyzing tRNA sequences and structures

Graphical summary of tRNA features

Description

gettRNAFeaturePlots generates a plot for every feature found with gettRNASummary. Based on the datatype, it will generate suitable point or bar plots. Names of the GRangesList will be used as sample identifiers and used for colouring.

The options tRNA_colour_palette, tRNA_colour_yes and tRNA_colour_no will be used for colours.

Usage

gettRNAFeaturePlots(x, plotScores = FALSE, scores = NA, scoreLabel = "Score")

## S4 method for signature 'GRangesList'
gettRNAFeaturePlots(x, plotScores = FALSE, scores = NA, scoreLabel = "Score")

Arguments

x	a named GRangesList object.
plotScores	logical value, whether to plot scores. If scores are not provided with an additional argument, it will try to use the column "score" of the GRanges objects.
scores	a list of scores, which have to have the same dimensions as the GRangesList or GRanges object.
scoreLabel	a string to use as a label for the x axis.

Value

a list of ggplot2 plots. These can be customized further.

Examples

data("gr", package = "tRNA")
data("gr_eco", package = "tRNA")
grl <- GRangesList(Sce = gr,
                   Eco = gr_eco)
plots <- gettRNAFeaturePlots(grl)

# customized plots
plots$length$layers <- plots$length$layers[c(-1,-2)]
plots$length + ggplot2::geom_boxplot()

FelixErnst/tRNA documentation built on April 1, 2024, 2:39 p.m.