new.trackdrawer: New Trackdrawer object

In jweile/mavevis: Visualization for MaveDB

New Trackdrawer object

Description

This constructor creates a new Trackdrawer object. The object can be used to draw a plot containing amino-acid resolution structural information tracks, such as conservation, secondary structure, solvent accessibility or burial.

Usage

new.trackdrawer(l, nox = FALSE)

Arguments

l	the length of the tracks (i.e. the number of amino acids)
nox	no x-axis. Removes the x-axis and decreases the bottom margin to 0. This option is for use with the layout() function, to support adding tracks on top of an existing graph that uses amino acid postion as the x-axis.

Details

The object has the following methods:

• add.track(values,label,col,minVal=0,maxVal=max(values)) adds a new numerical track, which will be visualized in heatmap style. values are the numerical values for the heatmap. label is the label that will be shown on the y-axis for this track. col is the color that will be used to generate the color ramp (from white to col). minVal is optional and is the minimum value that will be mapped to the color white (default 0). maxVal is also optional and is the maximum value in the scale, which will be mapped to col.

• add.constrack(values) adds a new conservation track, which will be visualized as a barplot. values are the conservation values to use.

• add.ss.track(values) adds a new secondary structure track, which will be visualized using spriral and arrow symbols. values are the character values representing the secondary structure type for each amino acid. Permissible values are: "AlphaHelix","H","G","I" for alpha helices, "Strand","E" for beta strands and "Disorder" for disordered regions. Any other string is interpreted as no specific secondary structure.

• draw() draws the plot

• num.tracks() returns the number of tracks currently added to the plot.

Value

an object of type TrackDrawer.

Examples

## Not run: 
td <- new.trackdrawer(50)
td$add.track(runif(50,0,1),"SASA","blue")
td$add.constrack(runif(50,0,11))
td$add.ss.track(sample(c("AlphaHelix","Strand",""),50,replace=TRUE))
td$draw()

## End(Not run)

jweile/mavevis documentation built on Oct. 30, 2023, 7:16 a.m.