heatmap: Visualize a connectivity matrix

In abnormally-distributed/rsfcNet: Analyze resting state functional connectivity networks

Description

Visualize a connectivity matrix

Usage

heatmap(
  graph,
  plot = TRUE,
  type = "static",
  save.html = FALSE,
  plot.title = "Network Heatmap",
  directory = paste0(getwd(), "/"),
  filename = "heatmap.html",
  color.scheme = viridis::viridis(500)
)

Arguments

graph	an igraph object or matrix
type	"static" (the default) creates a standard image, "html" creates an interactive image with plotly
save.html	Save the HTML file (only for type="html")
plot.title	A title for the image
directory	Where to save the HTML for a plotly image. Deaults to current working directory.
filename	What to call the html file
color.scheme	A color scheme. Defaults to viridis from the viridis package, a colorblind friendly palette.

Details

This creates a visualization of a connectivity matrix. Either a standard static image can be created or an interactive image with plotly can be created. Color palettes can be supplied that will work with either output type with packages such as viridis, colorRamps, grDevices, and RColorBrewer.

A few color palettes I recommend besides the default:

colorRamps::blue2red(500) , which is particuarly good for visualizing a contrast between positive and negative correlations

colorRamps::ygobb(500))

colorRamps::matlab.like(500)

colorRamps::matlab.like2(500)

viridis::magma(500)

viridis::plasma(500)

grDevices::grey.colors(500)

Author(s)

Brandon Vaughan

This creates a correlogram (heatmap) with plotly in html format.

abnormally-distributed/rsfcNet documentation built on March 8, 2020, 5:32 p.m.