The first argument of heat_tree()
, data
is now replaced with x
,
which can be a dataframe (or tibble), a party (or constparty) object
specifying the precomputed tree, or partynode object specifying the
customized tree. custom_tree
argument is no longer needed.
Please make sure your version of R >= 3.5.0 before installation.
You can install the released version of treeheatr from CRAN with:
install.packages('treeheatr')
Or the development version from GitHub with remotes:
# install.packages('remotes') # uncomment to install devtools
remotes::install_github('trang1618/treeheatr')
Classification of different types of penguin species.
library(treeheatr)
heat_tree(penguins, target_lab = 'species')
Classification of different cultivars of wine.
heat_tree(wine, target_lab = 'Type', target_lab_disp = 'Cultivar')
If you use treeheatr in a scientific publication, please consider citing the following paper:
Le TT, Moore JH. treeheatr: an R package for interpretable decision tree visualizations. Bioinformatics. 2020 Jan 1.
BibTeX entry:
@article{le2020treeheatr,
title={treeheatr: an R package for interpretable decision tree visualizations},
author={Le, Trang T and Moore, Jason H},
journal={Bioinformatics},
year={2020},
doi="10.1093/bioinformatics/btaa662"
}
treeheatr incorporates a heatmap at the terminal node of your decision tree. The basic building blocks to a treeheatr plot are (yes, you guessed it!) a decision tree and a heatmap.
The decision tree is computed with partykit::ctree()
and plotted
with the well-documented and flexible
ggparty package.
The tree parameters can be passed to ggparty functions via the
heat_tree()
and draw_tree()
functions of treeheatr. More
details on different ggparty geoms can be found
here.
The heatmap is shown with ggplot2::geom_tile()
. The user may
choose to cluster the samples within each leaf node or the features
across all samples.
Make sure to check out the vignette for detailed information on the usage of treeheatr.
Please open an issue for questions related to treeheatr usage, bug reports or general inquiries.
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