CorrHeatmap: Plot correlation heatmap

In Mathelab/IntLIM: Integration of Omics Data Using Linear Modeling

Plot correlation heatmap

Description

Plot correlation heatmap

Usage

CorrHeatmap(inputResults, viewer = T, top_pairs = 1200, treecuts = 2,
  palette = NULL, static = FALSE, html.file = NULL,
  pdf.file = NULL)

Arguments

inputResults	IntLimResults object (output of ProcessResults())
viewer	whether the plot should be displayed in the RStudio viewer (T) or in Shiny/Knittr (F)
top_pairs	cutoff of the top pairs, sorted by adjusted p-values, to be plotted (plotting more than 1200 can take some time) (default: 1200)
treecuts	number of clusters (of gene-metabolite pairs) to cut the tree into for color-coding
palette	choose an RColorBrewer palette ("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Paired", etc.) or submit a vector of colors
static	allows user to decide whether heatmap is interactive or static
html.file	allows user to specify file path to output heatmap onto (used for non-static heatmaply objects)
pdf.file	allows user to specify file path to output heatmap onto (used for static heatmap.2 objects)

Value

a highcharter object

Examples

## Not run: 
dir <- system.file("extdata", package="IntLIM", mustWork=TRUE)
csvfile <- file.path(dir, "NCItestinput.csv")
mydata <- ReadData(csvfile,metabid='id',geneid='id')
myres <- RunIntLim(mydata,stype="PBO_vs_Leukemia")
myres <- ProcessResults(myres,mydata)
CorrHeatmap(myres)

## End(Not run)

Mathelab/IntLIM documentation built on July 9, 2022, 5:10 p.m.