lpm_heatmap: Plot a heatmap.

In goat-anti-rabbit/labelpepmatch.R: Tools For Interpreting Mass Spectra With Labeled Peptides

Description

Make a heatmap from an lpm_linearmodel object. Uses the residuals of the null model of the lpm_linearmodel. This is a linear model with label as a main effect, without accounting for treatment. The lpm_heatmap function can be applied both on the raw residuals or on the contrasts within one peak pair.

Usage

lpm_heatmap(x, contrasts = F, prawcutoff = 0.05, padjcutoff = 0.05,
  FCcutoff = 1.25, main = "heatmap")

Arguments

x	An object of class lpm_linearmodel
contrasts	Logical. Should the heatmap be on the contrasts, or on the residuals?
prawcutoff	Numeric. Cutoff for maximal raw p-value for features to be retained in the heatmap.
padjcutoff	Numeric. Cutoff for maximal adjusted p-value for features to be retained in the heatmap.
FCcutoff	Numeric. Cutoff for minimal log2 fold change.
main	Character. Title of the heatmap.

Author(s)

Rik Verdonck

goat-anti-rabbit/labelpepmatch.R documentation built on May 17, 2019, 7:29 a.m.