aPEAR.theme {aPEAR}

Default theme configuration for aPEAR

Description

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

Usage

aPEAR.theme

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)

Value

an object of class aPEAR.theme.config

Examples

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

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