Package: OTclust 1.0.6

OTclust: Mean Partition, Uncertainty Assessment, Cluster Validation and Visualization Selection for Cluster Analysis

Providing mean partition for ensemble clustering by optimal transport alignment(OTA), uncertainty measures for both partition-wise and cluster-wise assessment and multiple visualization functions to show uncertainty, for instance, membership heat map and plot of covering point set. A partition refers to an overall clustering result. Jia Li, Beomseok Seo, and Lin Lin (2019) <doi:10.1002/sam.11418>. Lixiang Zhang, Lin Lin, and Jia Li (2020) <doi:10.1093/bioinformatics/btaa165>.

Authors:Lixiang Zhang [aut, cre], Beomseok Seo [aut], Lin Lin [aut], Jia Li [aut]

OTclust_1.0.6.tar.gz
OTclust_1.0.6.zip(r-4.7-x86_64)OTclust_1.0.6.zip(r-4.7-arm64)OTclust_1.0.6.zip(r-4.6-x86_64)OTclust_1.0.6.zip(r-4.6-arm64)OTclust_1.0.6.zip(r-4.5-x86_64)
OTclust_1.0.6.tgz(r-4.6-x86_64)OTclust_1.0.6.tgz(r-4.6-arm64)OTclust_1.0.6.tgz(r-4.5-x86_64)OTclust_1.0.6.tgz(r-4.5-arm64)
OTclust_1.0.6.tar.gz(r-4.7-arm64)OTclust_1.0.6.tar.gz(r-4.7-x86_64)OTclust_1.0.6.tar.gz(r-4.6-arm64)OTclust_1.0.6.tar.gz(r-4.6-x86_64)
OTclust_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OTclust/json (API)

# Install 'OTclust' in R:

install.packages('OTclust', repos = c('https://lixiangzhang.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lixiangzhang/otclust/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

sim1 - Simulated toy data
vis_pollen - Single cell gene visualization data from Pollen's paper
YAN - Single cell gene data from Yan's paper

On CRAN:

cpp

3.70 score 7 scripts 332 downloads 14 exports 20 dependencies

Last updated from:8070f0d0ff. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	139
linux-devel-x86_64	OK	135
source / vignettes	OK	266
linux-release-arm64	OK	134
linux-release-x86_64	OK	147
macos-release-arm64	OK	165
macos-release-x86_64	OK	375
macos-oldrel-arm64	OK	223
macos-oldrel-x86_64	OK	571
windows-devel-arm64	OK	399
windows-devel-x86_64	OK	139
windows-release-arm64	OK	332
windows-release-x86_64	OK	88
windows-oldrel-x86_64	OK	108
wasm-release	OK	141

Exports:align clustCPS cplot CPS ensemble jaccard mplot otclust otplot perturb pplot preprocess visCPS wassDist

Dependencies:class cli cpp11 farver ggplot2 glue gtable isoband labeling lifecycle magrittr R6 RColorBrewer Rcpp rlang S7 scales vctrs viridisLite withr

Quick tour of OTclust

Rendered fromOTclust.Rmdusingknitr::rmarkdown

Last update: 2023-09-25
Started: 2023-09-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Optimal Transport Alignment	align
CPS Analysis for cluster validation..	clustCPS
Covering Point Set Plot	cplot
CPS Analysis on a collection of clustering results	CPS
Generate an ensemble of partitions.	ensemble
Jaccard similarity matrix.	jaccard
Membership Heat Map	mplot
Mean partition by optimal transport alignment.	otclust
Visualize a partition on 2 dimensional space	otplot
Perturb data by adding noise, bootstrapping or mix-up	perturb
Point-wise Uncertainty Assessment	pplot
Data preprocessing	preprocess
Simulated toy data	sim1
Single cell gene visualization data from Pollen's paper	vis_pollen
CPS Analysis on selecting visualization method.	visCPS
Wasserstein distance between two partitions.	wassDist
Single cell gene data from Yan's paper	YAN