node.tight {gcExplorer}R Documentation

Node Methods for Neighborhood Graphs

Description

Several methods how to color nodes of a neighborhood graph.

Usage

## S4 method for signature 'kccasimple':
node.tight(object, theme, colscale)
## S4 method for signature 'kccasimple':
node.size(object, theme, colscale)
## S4 method for signature 'kccasimple':
node.go(object, theme, colscale, gonr, source.group, source.id, id)
## S4 method for signature 'kccasimple':
node.group(object, theme, colscale, group)
## S4 method for signature 'kccasimple':
legend.size(object, theme, colscale=NULL, pos="bottomleft")
## S4 method for signature 'kccasimple':
legend.tight(object, theme, colscale=NULL, pos="bottomleft")

Arguments

object An object of class "kccasimple"
theme A color theme, eg. theme="blue".
colscale Range of luminescence lum of hcl colors, default is min to max.
gonr Unique identifier from source.group giving the group of genes to be extracted.
source.id Vector of gene IDs assigned to functional groups given in source.group.
source.group Vector of the same length as source.id.
id Vector of identifiers of the same length as rows in the clustered data of the same type as given in source.id.
group Vector of integers giving the cluster membership of grouped genes.
pos Position where the legend should be placed.

Details

Function node.size is used to highlight large clusters where the largest cluster will be assigned the darkest color.

Function node.tight is used to highlight tight clusters where the tightest cluster will be assigned the darkest color.

Function node.go is used to highlight clusters with accumulation of the functional group given by gonr where the highest proportion will be assigned the darkest color.

Function node.group is used to highlight clusters with accumulation of a functional group where the class membership are passed by argument group. Again the highest proportion will be assigned the darkest color.

Author(s)

Theresa Scharl and Ingo Voglhuber

See Also

gcExplorer

Examples

data("hsod")
set.seed(1111)
cl1 <- qtclust(hsod, radius = 2, save.data = TRUE)

gcExplorer(cl1, theme = "blue", node.function = node.size, 
           legend.pos= "topleft")

gcExplorer(cl1, theme = "red", node.function = node.tight, 
           legend.pos= "topleft")

data("gobp")
gcExplorer(cl1, theme = "green", node.function = node.go, 
           node.args = list(gonr = "transport", source.group = gobp[,3],
                            source.id = gobp[,1], id = bn_hsod), 
           legend.pos= "topleft")


[Package gcExplorer version 0.9-1 Index]