dagHeatmap: Visualize daglogo using a heatmap.

In haibol2016/dagLogo: dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory

Description

Using a heatmap to visualize results of testing differential amino acid usage.

Usage

dagHeatmap(testDAUresults, type = c("diff", "statistics"), ...)

Arguments

testDAUresults	An object of testDAUresults-class, which contains results of testing differential amino acid usage.
type	A character vector of length 1, the type of metrics to display on y-axis. The available options are "diff" and "statistics", which are differences in amino acid usage at each position between the inputSet and the backgroundSet, and the Z-scores or odds ratios when Z-test or Fisher's exact test is performed to test the differential usage of amino acid at each position between the two sets.
...	other parameters passed to thepheatmap function.

Value

The output from the pheatmap function.

Author(s)

Jianhong Ou, Haibo Liu

Examples

data("seq.example")
data("proteome.example")
bg <- buildBackgroundModel(seq.example, proteome=proteome.example, 
                           numSubsamples=10)
t0 <- testDAU(seq.example, bg)
dagHeatmap(testDAUresults = t0, type = "diff")

haibol2016/dagLogo documentation built on June 28, 2020, 1:31 a.m.