makeLegends: Add a legend

In gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines

Description

Makes a legend object using ComplexHeatmap package which can then be plotted using the gmovizPlot function.

Usage

makeLegends(label_legend = FALSE, label_data = NULL,
  label_legend_title = "Gene Labels", feature_legend = FALSE,
  feature_data = NULL, feature_legend_title = "Features",
  scatterplot_legend = FALSE, scatterplot_legend_labels = c("Gains",
  "Losses"), point_colour = "black", point_outline_colour = "black",
  point_type = 21, scatterplot_legend_title = "Copy Number Variants",
  linegraph_legend = FALSE,
  linegraph_legend_labels = "Per Base Coverage",
  linegraph_legend_colours = "black",
  linegraph_legend_title = "Line Graph", background_colour = "white")

Arguments

label_legend	Whether to make a legend for labels (good for colour-coded labels).
label_data	The label data.
label_legend_title	Title for the label legend.
feature_legend	Whether to make a legend for features.
feature_data	The feature data to use for the feature legend.
feature_legend_title	Title for the features legend.
scatterplot_legend	Whether to make a legend for the scatterplot track.
scatterplot_legend_labels	A vector of the name/description of each point e.g. if a point represents methylation, use 'methylation'. If we have red/blue points for copy number gain/loss use c('gain', 'loss').
point_type, point_colour, point_outline_colour	The type and colour of points, as supplied to the drawScatterplotTrack function.
scatterplot_legend_title	Title for scatterplot track legend.
linegraph_legend	Whether to plot a legend for a line graph track.
linegraph_legend_labels	A vector of label(s) for what the line graph means (e.g. 'Per Base Coverage' for a line graph track showing coverage).
linegraph_legend_colours	The colour of to the line graph track.
linegraph_legend_title	A title for the line graph legend.
background_colour	The colour of the background (either 'white' or 'black').

Value

An object of the Legends class.

See Also

If you want more customisation over your legends, please see https://jokergoo.github.io/circlize_book/book/legends.html for a detailed guide as to how to implement legends alongside the circlize plots. To plot these legends, see gmovizPlot

Examples

## a gene label legend
## the data
labels <- data.frame(chr=c('chr1', 'chr1'), start=c(100, 300),
end=c(150, 350), label=c('a', 'b'), type=c('gene', 'lncRNA'),
colour=c('red', 'blue'))

## making the legend
makeLegends(label_legend=TRUE, label_data=labels)

gmoviz documentation built on Nov. 8, 2020, 5:41 p.m.