Installation and loading dependencies | Introduction | Illustrative dataset | Pairwise sample Earth Mover's Distances | Calculating distances between samples | Individual marker contribution in the distance matrix | Metric Multidimensional scaling | Calculating the MDS projection | Plotting the MDS projection | Quality of projection - diagnostic tools | Additional options for the MDS projection | Aid to interpreting projection axes | Bi-plots | Bi-plot wrapping | Handling large datasets | Loading flow frames dynamically during distance matrix computation | Using BiocParallel to parallelize distance matrix computation | Expression matrices as input instead of flowFrames | Session information | References
Package: CytoMDS 1.9.0
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_1.9.0.tar.gz
CytoMDS_1.9.0.zip(r-4.7)CytoMDS_1.9.0.zip(r-4.6)CytoMDS_1.9.0.zip(r-4.5)
CytoMDS_1.9.0.tgz(r-4.6-any)CytoMDS_1.9.0.tgz(r-4.5-any)
CytoMDS_1.9.0.tar.gz(r-4.7-any)CytoMDS_1.9.0.tar.gz(r-4.6-any)
CytoMDS_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CytoMDS/json (API)
| # 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/docs site:https://uclouvain-cbio.github.io
On BioConductor:CytoMDS-1.9.0(bioc 3.24)CytoMDS-1.8.0(bioc 3.23)
flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization
Last updated from:12236215be. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 221 | ||
| linux-devel-x86_64 | NOTE | 495 | ||
| source / vignettes | OK | 442 | ||
| linux-release-x86_64 | NOTE | 489 | ||
| macos-release-arm64 | NOTE | 266 | ||
| macos-oldrel-arm64 | NOTE | 317 | ||
| windows-devel | NOTE | 511 | ||
| windows-release | NOTE | 493 | ||
| windows-oldrel | NOTE | 493 | ||
| wasm-release | OK | 233 |
Exports:as.matrixchannelSummaryStatscomputeMetricMDSdistByFeatureDistSumeigenValsEMDDistfeatureNamesfeatureNames<-ggplotDistFeatureImportanceggplotMarginalDensitiesggplotSampleMDSggplotSampleMDSShepardggplotSampleMDSWrapBiplotsggplotVolcanoGoFnDimnFeaturesnPointspairwiseEMDDistpctvarprojDistprojectionspwDistRSqRSqVecsmacofRessppstress
Dependencies:abindaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelbitbit64blobbootbroombslibcachemchangepointcheckmatecirclizeclassclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlcytolibCytoPipelinedata.tableDBIdbplyrDelayedArraydiagramdigestdir.expirydoParalleldplyre1071ellipseevaluatefarverfastmapfilelockflowAIflowCoreflowWorkspacefontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgdatagenericsGetoptLongggcytoggforceggplot2ggrepelglmnetGlobalOptionsgluegraphgridExtragtablegtoolshavenhexbinhighrHmischmshtmlTablehtmltoolshtmlwidgetshttr2IRangesisobanditeratorsjomojquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemicemimeminqamitmlncdfFlownlmenloptrnnetnnlsnumDerivopensslordinalpanpatchworkPeacoQCpillarpkgconfigplotrixplyrpngpolyclippolynompracmaprettyunitsprogressproxypurrrR6rappdirsRBGLrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreformulasreshape2RgraphvizRhdf5librjsonrlangrmarkdownrpartRProtoBufLibRSQLiterstudioapiS4ArraysS4VectorsS7sassscalesshapesmacofsnowSparseArraystringistringrsurvivalsyssystemfontstibbletidyrtidyselecttinytextransporttweenrtzdbucminfutf8vctrsviridisLitevroomweightswithrwordcloudxfunXMLXVectoryamlzoo
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 |
| standard volcano plot | ggplotVolcano |
| 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 |