makeAnnotationTrack {GenomeGraphs} | R Documentation

## Create objects of class AnnotationTrack

### 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)

[Package GenomeGraphs version 1.4.1 Index]