seqLogoGrid: Draw a motif logo on an existing viewport

Description Usage Arguments Details

View source: R/plot.R

Description

This function comes from the seqLogo package. It has been modified to remove some unneccessary code as suggested by W Huber (https://stat.ethz.ch/pipermail/bioconductor/2010-September/035267.html).

Usage

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  seqLogoGrid(pwm, ic.scale = TRUE, xaxis = TRUE,
    yaxis = TRUE, xfontsize = 10, yfontsize = 10,
    xmargin.scale = 1, ymargin.scale = 1, title = "",
    titlefontsize = 15)

Arguments

pwm

numeric The 4xW position weight matrix.

ic.scale

logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.

xaxis

logical If TRUE, an X-axis will be plotted.

yaxis

logical If TRUE, a Y-axis will be plotted.

xfontsize

numeric Font size to be used for the X-axis.

yfontsize

numeric Font size to be used for the Y-axis.

xmargin.scale

the scaling parameter for the X-axis margin. Useful when plotting more than one logo on a page

ymargin.scale

the scaling parameter for the Y-axis margin. Useful when plotting more than one logo on a page

title

to be shown on the top

titlefontsize

the fontsize of the title

Details

Use this function for more advanced plotting where the viewports are directly set up and maintained (see package grid).


PWMEnrich documentation built on May 2, 2018, 4:20 a.m.