SourceSet (version 0.1.0)

sourceCytoscape: Visualize in Cytoscape a collection of graphs analyzed with the source set algorithm

Description

The function, thanks to the connection with the Cytoscape software, allows the user to create a collection of graphs to be visualized in a unique session, while documenting interesting findings.

Usage

sourceCytoscape(sourceObj, name.graphs = names(sourceObj),
  collection.name = "SourceCollection", map.name.variable = NULL,
  method = "bonferroni")

Arguments

sourceObj

a SourceSetObj objects, i.e. the output of the sourceSet function.

name.graphs

the names of the graphs to be visualized. Default value is names(sourceObj). NOTE: even if a subset of graphs are selected in name.graphs, the returned statistics are always calculated on the entire collection in the sourceObj argument.

collection.name

name of the collection of graphs displayed in Cytoscape.

map.name.variable

a list of customized labels to be associated with the names of the genes. Each list element must contain only one value (i.e. the new label), and the name of each element must be associated with the names of the genes given as input to the sourceSet function (column names of data input argument). If a label is not mapped, the original name is used.

method

correction method for p-values calculated on graphs. The adjustment methods allowed are: fdr (default), holm, hochberg, hommel, bonferroni, BH, BY or none. For more details refer to p.adjust.

Details

The visual node attributes size and fill color are defined in a dynamic manner through a visual mapping based on the indices provided by the infoSource function (automatically uploaded in the bottom panel - right side).

A discrete mapper between source attribute and size is applied:

• big size: the variable belongs to the primary set (source=2);

• medium size: the variable belongs to the secondary set (source=1);

• small size: otherwise (source=0).

On the other hand, a color gradient mapper between fill node color and relevance is adopted: higher values are highlighted with darker blue color.

The default style can be changed manually either within Cytoscape (for further information see manual) or within an R package r2cytoscape through network SUID returned by the sourceCytoscape function (for further details see manual).

It is also possible to call the sourceCytoscape function multiple times, with all the graphs being visualized in a unique session within a collection specified by collection.name.

See Also

sourceSet, infoSource. sourceUnionCytoscape, r2cytoscape

Examples

# NOT RUN {
## Load the SourceSetObj obtained from the source set analysis of ALL dataset

# see vignette for more details
print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
class(results.all)

## NB: Remember to launch cytoscape before running the following commands
# Create two collections of pathways to visualize the results
graph.signaling<-names(results.all)[grep("signaling",names(results.all))]
graph.other<-setdiff(names(results.all),graph.signaling)

## Signaling collection
# }
# NOT RUN {
cytoID.signaling<-sourceCytoscape(results.all,
    name.graphs = graph.signaling, collection.name ="SignalingPathway")
# }
# NOT RUN {
## Other collection
# }
# NOT RUN {
cytoID.other<-sourceCytoscape(results.all,
    name.graphs = graph.other, collection.name ="OtherPathway")
# }