Package: CytoMDS 1.3.3
Philippe Hauchamps
CytoMDS: Low Dimensions projection of cytometry samples
This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.
Authors:
CytoMDS_1.3.3.tar.gz
CytoMDS_1.3.3.zip(r-4.5)CytoMDS_1.3.3.zip(r-4.4)CytoMDS_1.1.3.zip(r-4.3)
CytoMDS_1.3.3.tgz(r-4.4-any)CytoMDS_1.1.3.tgz(r-4.3-any)
CytoMDS_1.3.3.tar.gz(r-4.5-noble)CytoMDS_1.3.3.tar.gz(r-4.4-noble)
CytoMDS_1.3.3.tgz(r-4.4-emscripten)CytoMDS_1.1.3.tgz(r-4.3-emscripten)
CytoMDS.pdf |CytoMDS.html✨
CytoMDS/json (API)
NEWS
| # Install 'CytoMDS' in R: |
| install.packages('CytoMDS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/uclouvain-cbio/cytomds/issues
Pkgdown:https://uclouvain-cbio.github.io
On BioConductor:CytoMDS-1.3.2(bioc 3.21)CytoMDS-1.2.0(bioc 3.20)
flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization
Last updated 18 hours agofrom:7214442f21. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 10 2024 |
| R-4.5-win | NOTE | Dec 10 2024 |
| R-4.5-linux | NOTE | Dec 10 2024 |
| R-4.4-win | NOTE | Dec 10 2024 |
| R-4.4-mac | NOTE | Dec 10 2024 |
| R-4.3-win | NOTE | Sep 24 2024 |
| R-4.3-mac | NOTE | Sep 24 2024 |
Exports:as.matrixchannelSummaryStatscomputeMetricMDSdistByFeatureDistSumeigenValsEMDDistfeatureNamesfeatureNames<-ggplotDistFeatureImportanceggplotMarginalDensitiesggplotSampleMDSggplotSampleMDSShepardggplotSampleMDSWrapBiplotsGoFnDimnFeaturesnPointspairwiseEMDDistpctvarprojDistprojectionspwDistRSqRSqVecsmacofRessppstress
Dependencies:abindaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootbroombslibcachemchangepointcheckmatecirclizeclassclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlcytolibCytoPipelinedata.tableDBIdbplyrDelayedArraydiagramdigestdoParalleldplyre1071ellipseevaluatefansifarverfastmapfilelockflowAIflowCoreflowWorkspacefontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgdatagenericsGetoptLongggcytoggforceggplot2ggrepelglmnetGlobalOptionsgluegraphgridExtragtablegtoolshavenhexbinhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjomojquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicemimeminqamitmlmunsellncdfFlownlmenloptrnnetnnlsnumDerivopensslordinalpanpatchworkPeacoQCpillarpkgconfigplogrplotrixplyrpngpolyclippolynompracmaprettyunitsprogressproxypurrrR6rappdirsRBGLRColorBrewerRcppRcppEigenreadrreshape2RgraphvizRhdf5librjsonrlangrmarkdownrpartRProtoBufLibRSQLiterstudioapiS4ArraysS4VectorssassscalesshapesmacofsnowSparseArraystringistringrsurvivalsyssystemfontstibbletidyrtidyselecttinytextransporttweenrtzdbucminfutf8vctrsviridisviridisLitevroomweightswithrwordcloudxfunXMLXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Summary statistics per channel computation | channelSummaryStats |
| metric MDS projection of sample | computeMetricMDS |
| DistSum class | as.matrix,DistSum-method colnames,DistSum-method colnames<-,DistSum-method dim,DistSum-method dimnames,DistSum-method dimnames<-,DistSum,ANY-method dimnames<-,DistSum,list-method distByFeature DistSum DistSum,list-method DistSum,matrix-method DistSum-class featureNames,DistSum-method featureNames<-,DistSum-method ncol,DistSum-method nFeatures nrow,DistSum-method rownames,DistSum-method rownames<-,DistSum-method show,DistSum-method [,DistSum,ANY,ANY,ANY-method [,DistSum,ANY,ANY,missing-method [,DistSum,ANY,missing,ANY-method [,DistSum,ANY,missing,missing-method |
| Calculate Earth Mover's distance between two samples | EMDDist |
| Plot of feature relative importance in distance | ggplotDistFeatureImportance |
| Plot of channel intensity marginal densities | ggplotMarginalDensities |
| Plot of Metric MDS object | ggplotSampleMDS |
| Plot of Metric MDS object - Shepard diagram | ggplotSampleMDSShepard |
| SampleMDS biplot wrapping | ggplotSampleMDSWrapBiplots |
| MDS class | eigenVals GoF MDS-class nDim nPoints pctvar projDist projections pwDist RSq RSqVec show,MDS-method smacofRes spp stress |
| Pairwise Earth Mover's Distance calculation | pairwiseEMDDist |