makeAnnotationTrack: Create objects of class AnnotationTrack

In GenomeGraphs: Plotting genomic information from Ensembl

Description

Convenience function for constructing objects of class AnnotationTrack.

Usage

makeAnnotationTrack(regions = NULL, chr = NULL, strand = NULL, start = NULL, end = NULL, feature = NULL, group = NULL, ID = NULL, dp = NULL)

Arguments

regions	A dataframe with columns start, end, feature, group, ID. start and end delineate the boundaries of the boxes feature can be used to color the boxes. Group denotes linking so generally exons from a gene form a group. Finally, ID can be used to plot names on boxes.
chr	The chromosome of the regions (can be ignored)
strand	The strand of the regions (can be ingored)
start	If regions is missing then we construct a dataframe from the remaining parameters.
end	Construct regions with this vector
feature	Construct regions with this feature vector or scalar
group	Defines a grouping
ID	Defines an ID for each annotation bit
dp	DisplayPars, in this case we can create a mapping between feature and color. So lets say in the feature column you have: gene, transcript, gene, then in the dp you can say gene = 'blue' and transcript = 'green'

Value

Returns an object of class AnnotationTrack

Examples

a <-  makeAnnotationTrack(start = c(10, 15, 25), end = c(12, 19, 31),
                      group = c(1,1,2), feature = c("gene", "gene", "tf"),
                      ID = paste("id", 1:3, sep = ""), dp = DisplayPars(gene = 'blue'))
gdPlot(a, minBase = 0, maxBase = 40)

GenomeGraphs documentation built on Oct. 31, 2019, 4:34 a.m.