neatmaps (version 1.1.0)

neatmap: Heatmap of Networks

Description

neatmap produces a heatmap of networks and their characteristics

Usage

neatmap(df, scale.df, link.method = "average", dist.method = "euclidean",
  nBootRep = 1000, mainTitle = "", xlabel, ylabel, xlabCex = 5,
  ylabCex = 5, heatmapMargins = c(50, 50, 50, 100))

Arguments

df

a dataframe of network attributes containing only numeric values

scale.df

A string indicating whether the data frame should be scaled, and if so, which method should be used. The options are "none", "basic", "normalize" and "percentize". If "none" is selected, then no scaling takes place. If "basic" is selected, each column is reduced to the 0-1 interval, whithout changing the underlying distribution. If "normalize" is selected, each column is normalized to have a mean of 0 and standard deviation of 1. If "percentize" is selected, column values are transformed into percentiles. This conserves the underlying distribution of the data if the data is not expected to be normally distributed.

link.method

The agglomeration method to be used. See method in hclust.

dist.method

The distance measure to be used. See method in dist.

nBootRep

The number of bootstrap replications for the statistical analysis of the hierarchical clustering. See pvclust.

mainTitle

The title of the heatmap.

xlabel

The x axis label of the heatmap.

ylabel

The y axis label of the heatmap.

xlabCex

The font size of the elements on the x axis.

ylabCex

The font size of the elements on the y axis.

heatmapMargins

The size of the margins for the heatmap. See heatmaply.

Value

A list containing the dendrogram of the hierarchical clustering, the significant clusters of the statistical analysis, the results of the statistical analysis and the heatmap.

Details

This function generates a heatmap of networks and their various characteristics from a data frame containing only numeric variables. These numeric values are then scaled using a chosen method. The hierarchical cluster analysis results used in the heatmap are also output. The heatmap is produced using the heatmaply package.

Examples

# NOT RUN {
df <- netsDataFrame(net.attr.df = networkAttrDF,
                    node.attr.df = nodeAttrDF,
                    edge.df = edgeDF)
heatmap <- neatmap(df, scale.df = "basic", mainTitle = "Heatmap", 
                   xlabel = "Chararacteritics", ylabel = "Networks",
                   link.method = "single", dist.method = "euclidean",
                   nBootRep = 10)

# }