readHDF5Ztree: readHDF5Ztree
In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality
readHDF5Ztree R Documentation
readHDF5Ztree
Description
Read the Ztree (scipy matrix representarion of a hierarchical clustering)
contained in a 10X single-cell CNV HDF5 file and return a
valid R hclust object representing the same tree.
More info on the Ztree matrix: https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-and-dendrogram-tutorial/
Usage
readHDF5Ztree(hdf5.file)
Arguments
hdf5.file
(H5IdComponent object) The result of opening an HDF5 file
with rhdf5::H5Fopen(data.file). The file must contain a "tree" element
with Ztree. For example, HDF5 files for CNV data produced by 10X CellRanger.
Value
A valid hclust object (standard R hierarchical clustering results)
Examples
not.run <- TRUE #We have no valid hdf5 file small enough to fit in a package
#Not Run
#data.file <- "path to a single-cell CNV data file"
#open.file <- rhdf5::H5Fopen(data.file)
#hc.tree <- readHDF5Ztree(open.file)
bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.
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| readHDF5Ztree | R Documentation |
readHDF5Ztree
Description
Read the Ztree (scipy matrix representarion of a hierarchical clustering) contained in a 10X single-cell CNV HDF5 file and return a valid R hclust object representing the same tree.
More info on the Ztree matrix: https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-and-dendrogram-tutorial/
Usage
readHDF5Ztree(hdf5.file)
Arguments
hdf5.file |
(H5IdComponent object) The result of opening an HDF5 file with rhdf5::H5Fopen(data.file). The file must contain a "tree" element with Ztree. For example, HDF5 files for CNV data produced by 10X CellRanger. |
Value
A valid hclust object (standard R hierarchical clustering results)
Examples
not.run <- TRUE #We have no valid hdf5 file small enough to fit in a package
#Not Run
#data.file <- "path to a single-cell CNV data file"
#open.file <- rhdf5::H5Fopen(data.file)
#hc.tree <- readHDF5Ztree(open.file)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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