node.tight {gcExplorer} | R Documentation |
Several methods how to color nodes of a neighborhood graph.
## 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")
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. |
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.
Theresa Scharl and Ingo Voglhuber
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")