aPEAR (version 1.0.0)

aPEAR.theme: Default theme configuration for aPEAR

Description

A list with parameters for customizing the theme of the enrichment network plot.

Usage

aPEAR.theme

Value

an object of class aPEAR.theme.config

Format

An object of class aPEAR.theme.config of length 9.

Details

colorBy: which column in the data should be used to color the nodes in the enrichment network plot (default: 'NES')

nodeSize: which column in the data should be used to get the node size for the enrichment network plot (default: 'setSize')

innerCutoff: similarity cutoff for within-cluster nodes (default: 0.1). Decreasing this value results in greater connectivity within the nodes in the same cluster. For example, innerCutoff = 0 would display all connections within the same cluster.

outerCutoff: similarity cutoff for between-cluster nodes (default: 0.5). Decreasing this value results in greater connectivity between the nodes in different clusters. For example, outerCutoff = 0 would display all connections between different clusters.

colorType: how to colour the nodes: 'nes' - will center around 0 with blue min and red max, 'pval' - will use log transform on the colorBy column and adjust color range (default: 'nes')

pCutoff: adjust p-value colouring cutoff when using colorType = 'pval' (default: -10)

drawEllipses: enable / disable ellipse drawing (default: FALSE)

fontSize: adjust cluster label font size (default: 3)

repelLabels: whether the cluster label positions should be corrected (default: FALSE)

Examples

# Display the default theme configuration used by aPEAR
aPEAR.theme

# Update the theme to draw ellipses
settings <- aPEAR.theme
settings$drawEllipses <- TRUE
settings