GSNA (version 0.1.4.2)

gsnDendroSubnetColors: gsnDendroSubnetColors, gsnDendroSubnetColors_dark

Description

Given a list of vectors of gene set IDs corresponding to subnets, returns a vector of colors. with each color corresponding to a subnet (see details).

Usage

gsnDendroSubnetColors(subnets)
gsnDendroSubnetColors_dark(subnets)

Value

A vector of colors with names corresponding to subnet names.

Arguments

subnets

A list of vectors containing, as elements, vectors corresponding to subnets and containing gene set IDs as subnet members. List element names are the names of the subnets. This corresponds to the set of subnets stored in the $distances[[distance]]$subnets field of a pared GSNData object.

Details

Given a list of vectors in which each vector contains a set of gene set IDs corresponding to a subnet, with list element names being the subnet names, this function generates a vector of colors in which subnets with a single member are colored black and subnets with multiple members are given associated distinct colors. In the returned vector of names, the names are the subnets and the elements are the associated colors. This function is primarily for generating colors for hierarchical dendrograms.

The gsnDendroSubnetColors() and gsnDendroSubnetColors_dark() do approximately the same thing, but gsnDendroSubnetColors_dark() returns a darker palette of colors.

Examples

library( GSNA )

# After gsnAssignSubnets() has been called, a list containing subnet
# assignments is stored in GSNData objects at
# object$distances[[distance]]$subnets

# It has this structure:
subnets <- list( `1` = c( "M30131", "M40742", "M29968", "M29984", "M29922",
                          "M30190", "M40775", "M30171", "M30154", "M30186" ),
                 `2` = c( "M40770" ),
                 `3` = c( "M30055", "M30117" ),
                 `4` = c( "M40804" ),
                 `5` = c( "M40776" ),
                 `6` = c( "M40846" ) )

# Based on this, singltons, subnets/clusters with single membership
# are assigned black, and subnets with multiple members are assigned
# colors using a color wheel:
colors_v <- gsnDendroSubnetColors( subnets )

# gsnDendroSubnetColors_dark does the same thing as
# gsnDendroSubnetColors, but picks darker colors.
dark_colors_v <- gsnDendroSubnetColors_dark( subnets )