Gates/filters in Flow Cytometry Data Visualization | abstract | Introduction | Filters and filter results | Visualization | Example Data | Filters in scatter plots | Simple Geometric Filter Types | Data-Driven Filters | Filters in one-dimensional density plots | Plotting parameters | Restrictions on the formula interface | Filters in parallel coodinate plots
Package: flowViz 1.77.0
Mike Jiang
flowViz: Visualization for flow cytometry
Provides visualization tools for flow cytometry data.
Authors:
flowViz_1.77.0.tar.gz
flowViz_1.77.0.zip(r-4.7)flowViz_1.77.0.zip(r-4.6)flowViz_1.77.0.zip(r-4.5)
flowViz_1.77.0.tgz(r-4.6-any)flowViz_1.77.0.tgz(r-4.5-any)
flowViz_1.77.0.tar.gz(r-4.7-any)flowViz_1.77.0.tar.gz(r-4.6-any)
flowViz_1.77.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowViz/json (API)
| # Install 'flowViz' in R: |
| install.packages('flowViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:flowViz-1.77.0(bioc 3.24)flowViz-1.76.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyinfrastructureflowcytometrycellbasedassaysvisualization
Last updated from:e3fb894be4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 190 | ||
| linux-devel-x86_64 | NOTE | 308 | ||
| source / vignettes | OK | 283 | ||
| linux-release-x86_64 | NOTE | 252 | ||
| macos-release-arm64 | NOTE | 130 | ||
| macos-oldrel-arm64 | NOTE | 118 | ||
| windows-devel | NOTE | 178 | ||
| windows-release | NOTE | 179 | ||
| windows-oldrel | NOTE | 206 | ||
| wasm-release | OK | 177 |
Exports:addNamecontourdensityplotecdfplotflowPlotflowViz.par.getflowViz.par.setglinesglpointsglpolygongpointsgpolygonhistogramlevelplotpanel.densityplot.flowset.stackpanel.ecdfplot.flowsetpanel.xyplot.flowframepanel.xyplot.flowframe.timepanel.xyplot.flowsetparallelplotprepanel.densityplot.flowset.stackprepanel.ecdfplot.flowsetprepanel.xyplot.flowframeprepanel.xyplot.flowframe.timeprepanel.xyplot.flowsetqqmathsplomtimelineplottimeLinePlotxyplot
Dependencies:BHBiobaseBiocGenericsbiocmakecpp11cytolibdeldirdir.expiryfilelockflowCoregenericshexbinIDPmiscinterpjpegKernSmoothlatticelatticeExtraMASSmatrixStatspngRColorBrewerRcppRcppEigenRhdf5libRProtoBufLibS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Visualization for flow cytometry | flowViz-package flowViz |
| convert a single flowFrame or a list of flowFrames to a list of flowSet | .process_flowFrame_overlay |
| extract the respective flowFrame from each flowSet based on the given sampleName | .process_overlay_flowSet |
| Add gate names to a flowViz plot. | addName addName,curv1Filter,character-method addName,curv1Filter,logical-method addName,curv2Filter,character-method addName,curv2Filter,logical-method addName,ellipsoidGate,character-method addName,ellipsoidGate,logical-method addName,kmeansFilter,character-method addName,kmeansFilter,logical-method addName,polygonGate,character-method addName,polygonGate,logical-method addName,quadGate,character-method addName,quadGate,logical-method addName,quadGate,matrix-method addName,rectangleGate,character-method addName,rectangleGate,logical-method addName-methods |
| Contour plots for flow data | contour contour,ANY-method contour,flowFrame-method contour,flowSet-method contour-methods |
| One-dimensional density/histogram plots for flow data | densityplot densityplot,formula,flowFrame-method densityplot,formula,flowSet-method densityplot,formula,ncdfFlowList-method densityplot,formula,ncdfFlowSet-method densityplot,formula,view-method histogram,formula,flowFrame-method histogram,formula,flowSet-method histogram,formula,ncdfFlowList-method histogram,formula,ncdfFlowSet-method panel.densityplot.flowset.stack prepanel.densityplot.flowset.stack |
| Standard Plots for Flow Cytometry Data | flowPlot flowPlot,flowFrame-method |
| Query and set session-wide graphical parameter defaults. | flowViz.par.get flowViz.par.set |
| Drawing filter boundaries | glines glines,curv1Filter,ANY-method glines,curv1Filter,flowFrame-method glines,curv1Filter,missing-method glines,curv1Filter,multipleFilterResult-method glines,curv2Filter,ANY-method glines,curv2Filter,flowFrame-method glines,curv2Filter,multipleFilterResult-method glines,ellipsoidGate,character-method glines,ellipsoidGate,filterResult-method glines,ellipsoidGate,flowFrame-method glines,filter,missing-method glines,filterResult,ANY-method glines,filterResult,flowFrame-method glines,kmeansFilter,ANY-method glines,norm2Filter,ANY-method glines,norm2Filter,flowFrame-method glines,norm2Filter,flowStats-method glines,norm2Filter,logicalFilterResult-method glines,polygonGate,character-method glines,polygonGate,filterResult-method glines,polygonGate,flowFrame-method glines,quadGate,character-method glines,quadGate,filterResult-method glines,quadGate,flowFrame-method glines,rectangleGate,character-method glines,rectangleGate,filterResult-method glines,rectangleGate,flowFrame-method glines-methods |
| Adding points within a gate to a plot | glpoints glpoints,curv1Filter,flowFrame,character-method glpoints,curv2Filter,flowFrame,character-method glpoints,ellipsoidGate,flowFrame,character-method glpoints,filter,flowFrame,missing-method glpoints,filter,missing,ANY-method glpoints,filterResult,flowFrame,ANY-method glpoints,filterResult,flowFrame,character-method glpoints,kmeansFilter,flowFrame,character-method glpoints,norm2Filter,flowFrame,character-method glpoints,polygonGate,flowFrame,character-method glpoints,quadGate,flowFrame,character-method glpoints,rectangleGate,flowFrame,character-method glpoints,subsetFilter,flowFrame,ANY-method glpoints-methods |
| Drawing filter regions | glpolygon glpolygon,complementFilter,ANY-method glpolygon,curv1Filter,ANY-method glpolygon,curv1Filter,flowFrame-method glpolygon,curv1Filter,missing-method glpolygon,curv1Filter,multipleFilterResult-method glpolygon,curv2Filter,ANY-method glpolygon,curv2Filter,flowFrame-method glpolygon,curv2Filter,multipleFilterResult-method glpolygon,ellipsoidGate,character-method glpolygon,ellipsoidGate,filterResult-method glpolygon,ellipsoidGate,flowFrame-method glpolygon,filter,missing-method glpolygon,filterResult,ANY-method glpolygon,filterResult,flowFrame-method glpolygon,filterResult,missing-method glpolygon,kmeansFilter,ANY-method glpolygon,norm2Filter,ANY-method glpolygon,norm2Filter,flowFrame-method glpolygon,norm2Filter,logicalFilterResult-method glpolygon,polygonGate,character-method glpolygon,polygonGate,filterResult-method glpolygon,polygonGate,flowFrame-method glpolygon,quadGate,character-method glpolygon,quadGate,filterResult-method glpolygon,quadGate,flowFrame-method glpolygon,rectangleGate,character-method glpolygon,rectangleGate,filterResult-method glpolygon,rectangleGate,flowFrame-method glpolygon,subsetFilter,ANY-method glpolygon-methods |
| Adding points within a gate to a plot | gpoints gpoints,curv1Filter,flowFrame,character-method gpoints,curv2Filter,flowFrame,character-method gpoints,filter,flowFrame,missing-method gpoints,filter,missing,ANY-method gpoints,filterResult,flowFrame,character-method gpoints,kmeansFilter,flowFrame,character-method gpoints,norm2Filter,flowFrame,character-method gpoints,polygonGate,flowFrame,character-method gpoints,quadGate,flowFrame,character-method gpoints,rectangleGate,flowFrame,character-method gpoints-methods |
| Drawing filter regions | gpolygon gpolygon,curv1Filter,ANY-method gpolygon,curv1Filter,flowFrame-method gpolygon,curv1Filter,missing-method gpolygon,curv1Filter,multipleFilterResult-method gpolygon,curv2Filter,ANY-method gpolygon,curv2Filter,flowFrame-method gpolygon,curv2Filter,multipleFilterResult-method gpolygon,ellipsoidGate,character-method gpolygon,ellipsoidGate,filterResult-method gpolygon,ellipsoidGate,flowFrame-method gpolygon,filter,missing-method gpolygon,filterResult,ANY-method gpolygon,filterResult,flowFrame-method gpolygon,kmeansFilter,ANY-method gpolygon,norm2Filter,ANY-method gpolygon,norm2Filter,flowFrame-method gpolygon,norm2Filter,logicalFilterResult-method gpolygon,polygonGate,character-method gpolygon,polygonGate,filterResult-method gpolygon,polygonGate,flowFrame-method gpolygon,quadGate,character-method gpolygon,quadGate,filterResult-method gpolygon,quadGate,flowFrame-method gpolygon,rectangleGate,character-method gpolygon,rectangleGate,filterResult-method gpolygon,rectangleGate,flowFrame-method gpolygon-methods |
| Methods implementing Lattice displays for flow data | lattice-methods levelplot,formula,flowSet-method parallel,flowFrame,missing-method parallel,formula,flowSet-method qqmath,formula,flowSet-method |
| Very basic plotting of flowFrames | plot plot,flowFrame,character-method plot,flowFrame,missing-method |
| Method implementing Lattice ECDF plots for flow data | ecdfplot ecdfplot,formula,flowSet-method panel.ecdfplot.flowset prepanel.ecdfplot.flowset |
| Method implementing Lattice scatter plot matrices for flow data. | panel.splom.flowframe splom splom,flowFrame,missing-method |
| Plot channel values against time | timeLinePlot timelineplot timeLinePlot,ANY,missing-method timeLinePlot,flowFrame,character-method timeLinePlot,flowSet,character-method |
| Methods implementing Lattice xyplots for flow data. | panel.xyplot.flowframe panel.xyplot.flowframe.time panel.xyplot.flowset prepanel.xyplot.flowframe prepanel.xyplot.flowframe.time prepanel.xyplot.flowset xyplot xyplot,flowFrame,missing-method xyplot,formula,flowFrame-method xyplot,formula,flowSet-method xyplot,formula,gateView-method xyplot,formula,ncdfFlowList-method xyplot,formula,ncdfFlowSet-method xyplot,formula,view-method xyplot,view,missing-method |
