Package: ggcyto 1.35.0
Mike Jiang
ggcyto: Visualize Cytometry data with ggplot
With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.
Authors:
ggcyto_1.35.0.tar.gz
ggcyto_1.35.0.zip(r-4.5)ggcyto_1.35.0.zip(r-4.4)ggcyto_1.35.0.zip(r-4.3)
ggcyto_1.35.0.tgz(r-4.4-any)ggcyto_1.33.0.tgz(r-4.3-any)
ggcyto_1.35.0.tar.gz(r-4.5-noble)ggcyto_1.35.0.tar.gz(r-4.4-noble)
ggcyto_1.35.0.tgz(r-4.4-emscripten)ggcyto_1.35.0.tgz(r-4.3-emscripten)
ggcyto.pdf |ggcyto.html✨
ggcyto/json (API)
NEWS
| # Install 'ggcyto' in R: |
| install.packages('ggcyto', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rglab/ggcyto/issues
On BioConductor:ggcyto-1.35.0(bioc 3.21)ggcyto-1.34.0(bioc 3.20)
immunooncologyflowcytometrycellbasedassaysinfrastructurevisualization
Last updated 2 months agofrom:21e5576c16. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 08 2024 |
| R-4.5-win | WARNING | Dec 08 2024 |
| R-4.5-linux | WARNING | Dec 08 2024 |
| R-4.4-win | WARNING | Dec 08 2024 |
| R-4.4-mac | WARNING | Dec 08 2024 |
| R-4.3-win | WARNING | Dec 08 2024 |
| R-4.3-mac | WARNING | Oct 28 2024 |
Exports:.fr2dt.fs2dt%+%as.ggplotautoplotaxis_x_inverse_transaxis_y_inverse_transcompute_statsfaust_gating_plotflowCore_asinht_transfortify_fsgate_nullgeom_gategeom_hvlinegeom_multi_rangegeom_overlaygeom_statsgetFlowFrameggcytoggcyto_arrangeggcyto_par_defaultggcyto_par_setis.ggcytois.ggcyto_flowSetis.ggcyto_parlabs_cytomarginalFilterprintrescale_gatescale_x_flowCore_fasinhscale_x_flowjo_biexpscale_x_flowJo_biexpscale_x_flowjo_fasinhscale_x_flowJo_fasinhscale_x_logiclescale_y_flowCore_fasinhscale_y_flowjo_biexpscale_y_flowJo_biexpscale_y_flowjo_fasinhscale_y_flowJo_fasinhscale_y_logicleshowstat_positionstats_nulltransform
Dependencies:abindBHBiobaseBiocGenericsclicolorspacecpp11crayoncytolibdata.tableDelayedArraydplyrfansifarverflowCoreflowWorkspacegenericsggplot2gluegraphgridExtragtablehexbinIRangesisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellncdfFlownlmepillarpkgconfigplyrR6RBGLRColorBrewerRcppRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsscalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVectorzlibbioc
ggcyto : Visualize Cytometry data with ggplot
Rendered fromTop_features_of_ggcyto.Rmdusingknitr::rmarkdownon Dec 08 2024.Last update: 2023-08-20
Started: 2016-05-16
Quick plot for cytometry data
Rendered fromautoplot.Rmdusingknitr::rmarkdownon Dec 08 2024.Last update: 2019-05-02
Started: 2015-05-05
Visualize flowSet with ggcyto
Rendered fromggcyto.flowSet.Rmdusingknitr::rmarkdownon Dec 08 2024.Last update: 2019-05-09
Started: 2015-05-15
Visualize GatingSet with ggcyto
Rendered fromggcyto.GatingSet.Rmdusingknitr::rmarkdownon Dec 08 2024.Last update: 2016-07-20
Started: 2015-05-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| It fortifies the data, fills some default settings and returns a regular ggplot object. | as.ggplot |
| Plot cytometry data in one or two dimension with the ggcyto package. | autoplot autoplot.cytoframe autoplot.cytoset autoplot.flowFrame autoplot.flowSet autoplot.GatingHierarchy autoplot.GatingSet autoplot.GatingSetList autoplot.ncdfFlowList |
| Display ggcyto axis labels using their raw values (as stored in the data structure) | axis_x_inverse_trans axis_y_inverse_trans |
| compute the statistics of the cell population defined by gates | compute_stats |
| plot faust gating schemes | faust_gating_plot |
| Inverse hyperbolic sine transformation(flowCore version). | flowCore_asinht_trans |
| Fortify a model into flowSet object | fortify_fs fortify_fs.cytoframe fortify_fs.default fortify_fs.flowFrame fortify_fs.flowSet fortify_fs.GatingSet fortify_fs.GatingSetList |
| Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table | fortify fortify.cytoframe fortify.cytoset fortify.flowFrame fortify.flowSet fortify.GatingSet fortify.GatingSetList fortify.ncdfFlowList |
| Convert a ellipsoidGate to a data.table useful for ggplot | fortify.ellipsoidGate |
| Convert a filterList to a data.table useful for ggplot | fortify.filterList |
| Convert a multiRangeGate to a data.table useful for ggplot | fortify.multiRangeGate |
| Convert a polygonGate to a data.table useful for ggplot | fortify.polygonGate |
| Convert a rectangleGate to a data.table useful for ggplot | fortify.rectangleGate |
| clear all the geom_gate() layer previously added | gate_null |
| Add a gate layer to a ggcyto plot. | geom_gate geom_gate.character geom_gate.default geom_gate.filter geom_gate.filterList geom_gate.filters geom_gate.filtersList geom_gate.list geom_gate.logical geom_gate.logicalFilterResult geom_gate.quadGate |
| Vertical or horizontal line. | geom_hvline |
| Draw multi-ranges as multiple rectangles on 1D or 2D plot | geom_multi_range |
| Overlay a population on an existing ggcyto plot analogous to backgating. | geom_overlay geom_overlay.character geom_overlay.default geom_overlay.flowFrame geom_overlay.flowSet geom_overlay.ncdfFlowList |
| Add a popluation statistics layer to a ggcyto plot. | geom_stats |
| extract flowFrame data structure from the given R object | getFlowFrame getFlowFrame.flowSet getFlowFrame.GatingHierarchy getFlowFrame.GatingSet getFlowFrame.GatingSetList getFlowFrame.ncdfFlowList |
| overloaded '+' method for ggcyto | + +,ggcyto_flowSet,ANY-method +,ggcyto_flowSet-method +,ggcyto_GatingLayout,ANY-method +,ggcyto_GatingLayout-method +,ggcyto_GatingSet,ANY-method +,ggcyto_GatingSet-method +.ggcyto_flowSet +.ggcyto_GatingLayout +.ggcyto_GatingSet +.ggcyto_ncdfFlowList ggcyto_add |
| Arrange a list of ggplot objects into gtable | ggcyto_arrange |
| Return The default ggcyto settings | ggcyto_par_default |
| Set some default parameters for ggcyto | ggcyto_par_set |
| Plot cytometry data using the ggcyto API | ggcyto ggcyto-class ggcyto.default ggcyto.flowSet ggcyto.GatingHierarchy ggcyto.GatingSet ggcyto.GatingSetList ggcyto_flowSet-class ggcyto_GatingLayout-class ggcyto_GatingSet-class |
| Reports whether x is a ggcyto object | is.ggcyto |
| Reports whether x is a ggcyto_flowSet object | is.ggcyto_flowSet |
| Reports whether x is a ggcyto_par object | is.ggcyto_par |
| Change axis labels and legend titles | labs_cyto |
| Generate a marginal gate. | marginalFilter |
| extend the original flowWorkspace:::.mergeGates function to restore quadGate when applicable | merge.quad.gates |
| Draw ggcyto on current graphics device. | plot.ggcyto print,ggcyto-method print.ggcyto show,ggcyto-method show.ggcyto |
| print method for ggcyto_gate_layout class | print.ggcyto_GatingLayout show,ggcyto_GatingLayout-method show.ggcyto_GatingLayout |
| replace current cytometry data | %+% %+%,ggcyto-method %+%,ggcyto_GatingLayout,ANY-method %+%,ggcyto_GatingLayout-method replace_data |
| Add a flowCore inverse hyperbolic sine scale to the x or y axes of a ggcyto plot. | scale_x_flowCore_fasinh scale_y_flowCore_fasinh |
| Add a logicle scale to the x or y axes of a ggcyto plot. | scale_x_logicle scale_y_logicle |
| Add a flowJo biexponential scale to the x or y axes of a ggcyto plot. | scales_flowjo_biexp scale_x_flowJo_biexp scale_x_flowjo_biexp scale_y_flowJo_biexp scale_y_flowjo_biexp |
| Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot. | scales_flowjo_fasinh scale_x_flowJo_fasinh scale_x_flowjo_fasinh scale_y_flowJo_fasinh scale_y_flowjo_fasinh |
| Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot. | stat_position stat_position.filter stat_position.filterList stat_position.list |
| clear all the geom_stats() layer previously added | stats_null |
| rescale methods for gates | rescale_gate rescale_gate.ellipsoidGate rescale_gate.polygonGate rescale_gate.quadGate rescale_gate.rectangleGate transform transform,filter-method transform,filterList-method transform-gate |
