Description Usage Arguments Value Functions Examples
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ## 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
:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 |
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)
|
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