gcExplorer {gcExplorer} | R Documentation |
Plot a neighborhood graph for "kccasimple"
cluster solutions.
## S4 method for signature 'kccasimple': gcExplorer(object, layout = c("dot", "neato", "twopi","circo","fdp"), theme = "grey", edge.method=c("orig","mean","min","max"), node.function = NULL, node.args = NULL, doViewPort = FALSE, filt = 0.1, interactive = !is.null(panel.function), dev=c("one","many"), panel.function = NULL, panel.args = NULL, bgdata = NULL, colscale = NULL, mfrow = c(1,1), legend.pos = "none")
object |
Object of class "kccasimple" . |
layout |
Layout method used: One of "dot" , "neato" , "twopi" , "circo" , and "fdp" . |
theme |
Color theme used. |
edge.method |
Several methods are available to draw edges: "orig" , "mean" ,
"min" , and "max" , see details below. |
node.function |
Optional. Additional information about the clusters can be included in the representation of nodes. Either a function calculating node colors or a grid-based function (see doViewPort ). |
node.args |
List of arguments which should be passed to node.function . |
doViewPort |
Currently not used in release version of the package. Call a grid-based function specified
by argument node.function and use it for node representation? |
filt |
Cutoff value for similarities between clusters, edges above the threshold will be displayed. |
interactive |
Should the plot be interactive? |
dev |
Only used if interactive=TRUE . Display each cluster plot (specified by panel.function ) in one device or open new devices for each cluster when clicking on a node. |
panel.function |
Only used if interactive=TRUE . The panel function
which should be used to display the corresponding cluster |
panel.args |
List of arguments which should be passed to panel.function . |
bgdata |
Background data to be plotted by panel.function or node.function . |
colscale |
A vector of length 2 specifying the color range for edges and nodes, e.g. c(0,0.5). |
mfrow |
Only used if interactive=TRUE . The panel layout in which the panel plots should be displayed. |
legend.pos |
Position of the legend. |
A neighborhood graph is the default plot method for cluster objects of
package flexclust
. For large and highdimensional data sets like
microarray data linear projection of the data into two dimensions may
not scale well in the number of clusters. In this case non-linear arrangement
of the nodes using layout algorithms from Graphviz can be helpful. An
interface to Graphviz is provided in Bioconductor package Rgraphviz
.
One of the implemented layout algorithms can be selected using layout
.
In a neighborhood graph each node corresponds to a cluster centroid.
Two nodes are connected by an edge if there exist data points that have
these two centroids as closest and second closest. The edge weights are
taken from clusterSim(object)
. The similarity between two clusters is
bounded between 0 and 1 where well-separated clusters have values close to 0.
The larger the similarity between clusters the stronger the edge will be
drawn in the graph. The cutoff value for drawing the edge between two
centroids can be chosen by argument filt
. The larger the filt value
the fewer edges will be drawn.
Originally the neighborhood graph is a directed graph. An edge will be
drawn from centroid 1 to centroid 2 if there exists at least one data
point that has centroid 1 as closest and centroid 2 as second closest.
But there need not necessarily be a data point that has centroid 2 as
closest and centroid 1 as second closest centroid. For this reason there
are several methods for plotting the edges between nodes. The default
edge.method
is 'orig' where each edge is drawn separately with
its corresponding weight. This method will result in a directed graph. All
other edge methods yield undirected graphs where the mean, minimum or maximum
of the similarities between two clusters is used.
Additional information about the clusters can be included in the graph using
node.function
and panel.function
. node.function
is used
for the node representation. If no node.function
is given all nodes
will be drawn in one color. The node.function
can be used to calculate
different colors for the nodes like cluster size or cluster tightness.
Additionally node.function
can be a grid–based function displaying
the data in the underlying cluster, e.g. a scatterplot or a boxplot.
gcExplorer
is implemented interactively. If interactive=TRUE
panel.function
is used to plot a cluster when clicking on the
corresponding node. An example of a panel.function
is given by function
gcProfile
.
Function calcHCL
is used to calculate a HCL–based color.
Object of class "graphdata"
with the following slots: an object of class
"Ragraph"
(see package Rgraphviz
), object
, bgdata
,
node.function
, edge.method
, theme
and colscale
.
Theresa Scharl and Ingo Voglhuber
Theresa Scharl and Friedrich Leisch. gcExplorer: Interactive Exploration of Gene Clusters. Bioinformatics, 25(8): 1089-1090, 2009.
data("hsod") cl1 <- qtclust(hsod, radius = 2, save.data = TRUE) gcExplorer(cl1, theme = "blue", node.function = node.size)