show,TreeViz-method {scTreeViz} | R Documentation |
show object
Method to aggregate a TreeViz object
Method to aggregate a TreeViz object
Generic method to register data to the epiviz data server
plot tree from TreeViz
## S4 method for signature 'TreeViz' show(object) aggregateTree(x, ...) ## S4 method for signature 'TreeViz' aggregateTree( x, selectedLevel = 3, selectedNodes = NULL, aggFun = colSums, start = 1, end = NULL, by = "row", format = "TreeViz" ) ## S4 method for signature 'TreeViz' register(object, tree = "row", columns = NULL, ...) ## S4 method for signature 'TreeViz,ANY' plot(x, y)
object |
The object to register to data server |
x |
treeviz object |
... |
Additional arguments passed to object constructors |
selectedLevel |
level to select nodes from |
selectedNodes |
used to set states on individual nodes to define a cut on the tree |
aggFun |
aggregate function to use, by default colSums if by="row", rowSums if by="col" |
start, end |
indices to filter nodes |
by |
"row" to aggregate the TreeIndex on rowData, "col" to aggregate TreeIndex on colData |
format |
return format can be one of "counts" or "TreeViz" |
tree |
Is tree over rows or columns of the object (default: "row") |
columns |
Name of columns containing data to register |
y |
none |
describe a TreeIndex object
a generic
a Treeviz object or type specified by format
An EpivizTreeData-class
object
Dataframe containing cluster information at different resolutions
show,TreeViz-method
:
aggregateTree
:
aggregateTree,TreeViz-method
:
register,TreeViz-method
:
plot,TreeViz,ANY-method
:
library(metagenomeSeq) data(mouseData) counts <- MRcounts(mouseData) hierarchy <- fData(mouseData) tree <- TreeIndex(hierarchy) mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree) aggregateTree(mbiome) library(metagenomeSeq) data(mouseData) counts <- MRcounts(mouseData) hierarchy <- fData(mouseData) tree <- TreeIndex(hierarchy) mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree) aggregateTree(mbiome) library(metagenomeSeq) data(mouseData) counts <- MRcounts(mouseData) hierarchy <- fData(mouseData) tree <- TreeIndex(hierarchy) mbiome <- TreeViz(SimpleList(counts=counts), rowData=tree) plot(mbiome)