ggcyto: Visualize Cytometry data with ggplot

With the dedicated fority 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.

AuthorMike Jiang
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.2.3
https://github.com/RGLab/ggcyto/issues

View on Bioconductor

Man pages

as.ggplot: It fortifies the data, fills some default settings and...

autoplot: Plot fluorescence intensity in one or two dimension.

axis_x_inverse_trans: Display axis labels in raw scales

compute_stats: compute the statistics of the cell population defined by...

fortify.ellipsoidGate: Convert a ellipsoidGate to a data.table useful for ggplot

fortify.filterList: Convert a filterList to a data.table useful for ggplot

fortify.flowSet: Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible...

fortify_fs: Fortify a model into flowSet object

fortify.polygonGate: Convert a polygonGate to a data.table useful for ggplot

fortify.rectangleGate: Convert a rectangleGate to a data.table useful for ggplot

geom_gate: add a flowCore gate layer

geom_overlay: Overlay other populations on existing plots.

geom_stats: Popluation statistics layer

getFlowFrame: extract flowFrame data structure from the given R object

ggcyto: Create a new ggcyto plot

ggcyto_arrange: Arrange a list of ggplot objects into gtable

ggcyto.flowSet: Create a new ggcyto plot from a flowSet

ggcyto_flowSet_add: overloaded '+' method for ggcyto

ggcyto.GatingSet: Create a new ggcyto plot from a GatingSet

ggcyto_GatingSet_add: overloaded '+' method for ggcyto.gs

ggcyto_par_default: Return The default ggcyto settings

ggcyto_par_set: Set some default parameters for ggcyto

is.ggcyto: Reports whether x is a ggcyto object

is.ggcyto_flowSet: Reports whether x is a ggcyto_flowSet object

is.ggcyto_par: Reports whether x is a ggcyto_par object

labs_cyto: Change axis labels and legend titles

marginalFilter: Generate a marginal gate.

plus-.ggcyto_GatingLayout: overloaded '+' method for ggcyto_gate_layout

print.ggcyto: Draw ggcyto on current graphics device.

print.ggcyto_GatingLayout: print method for ggcyto_gate_layout class

scale_x_flowJo_biexp: flowJo biexponential scale

scale_x_flowJo_fasinh: flowJo inverse hyperbolic sine scale

scale_x_logicle: flowJo inverse hyperbolic sine scale

stat_position: compute the positions of the population statistics based on...

Functions

as.ggplot Man page
autoplot.flowFrame Man page
autoplot.flowSet Man page
autoplot.GatingHierarchy Man page
autoplot.GatingSet Man page
autoplot.GatingSetList Man page
autoplot.ncdfFlowList Man page
axis_x_inverse_trans Man page
axis_y_inverse_trans Man page
compute_stats Man page
fortify Man page
fortify.ellipsoidGate Man page
fortify.filterList Man page
fortify.flowFrame Man page
fortify.flowSet Man page
fortify_fs Man page
fortify_fs.default Man page
fortify_fs.flowFrame Man page
fortify_fs.flowSet Man page
fortify_fs.GatingSet Man page
fortify_fs.GatingSetList Man page
fortify.GatingSet Man page
fortify.GatingSetList Man page
fortify.ncdfFlowList Man page
fortify.polygonGate Man page
fortify.rectangleGate Man page
geom_gate Man page
geom_gate.character Man page
geom_gate.default Man page
geom_gate.ellipsoidGate Man page
geom_gate.filterList Man page
geom_gate.filters Man page
geom_gate.filtersList Man page
geom_gate.list Man page
geom_gate.logical Man page
geom_gate.logicalFilterResult Man page
geom_gate.polygonGate Man page
geom_gate.rectangleGate Man page
geom_overlay Man page
geom_overlay.character Man page
geom_overlay.default Man page
geom_overlay.flowFrame Man page
geom_overlay.flowSet Man page
geom_stats Man page
getFlowFrame Man page
getFlowFrame.flowSet Man page
getFlowFrame.GatingHierarchy Man page
getFlowFrame.GatingSet Man page
getFlowFrame.GatingSetList Man page
getFlowFrame.ncdfFlowList Man page
ggcyto Man page
ggcyto_arrange Man page
ggcyto-class Man page
ggcyto.default Man page
+.ggcyto_flowSet Man page
ggcyto.flowSet Man page
+,ggcyto_flowSet,ANY-method Man page
ggcyto_flowSet-class Man page
ggcyto.GatingHierarchy Man page
+.ggcyto_GatingLayout Man page
+,ggcyto_GatingLayout,ANY-method Man page
ggcyto_GatingLayout-class Man page
+.ggcyto_GatingSet Man page
ggcyto.GatingSet Man page
+,ggcyto_GatingSet,ANY-method Man page
ggcyto_GatingSet-class Man page
ggcyto.GatingSetList Man page
ggcyto.ncdfFlowList Man page
ggcyto_par_default Man page
ggcyto_par_set Man page
is.ggcyto Man page
is.ggcyto_flowSet Man page
is.ggcyto_par Man page
labs_cyto Man page
marginalFilter Man page
plot.ggcyto Man page
print.ggcyto Man page
print.ggcyto_GatingLayout Man page
print,ggcyto-method Man page
scale_x_flowJo_biexp Man page
scale_x_flowJo_fasinh Man page
scale_x_logicle Man page
scale_y_flowJo_biexp Man page
scale_y_flowJo_fasinh Man page
scale_y_logicle Man page
show.ggcyto Man page
show.ggcyto_GatingLayout Man page
show,ggcyto_GatingLayout-method Man page
show,ggcyto-method Man page
stat_position Man page
stat_position.filter Man page
stat_position.filterList Man page
stat_position.list Man page

Files

ggcyto/DESCRIPTION
ggcyto/NAMESPACE
ggcyto/R
ggcyto/R/AllClasses.R ggcyto/R/autoplot.R ggcyto/R/axis_inverse_trans.R ggcyto/R/compute_stats.R ggcyto/R/fortify.R ggcyto/R/fortify_fs.R ggcyto/R/geom_gate.R ggcyto/R/geom_hvline.R ggcyto/R/geom_overlay.R ggcyto/R/geom_stats.R ggcyto/R/getFlowFrame.R ggcyto/R/ggcyto.R ggcyto/R/ggcyto_GatingLayout.R ggcyto/R/ggcyto_GatingSet.R ggcyto/R/ggcyto_flowSet.R ggcyto/R/ggcyto_par.R ggcyto/R/labs.R ggcyto/R/scales_flowJo_biexp.R ggcyto/R/scales_flowJo_fasinh.R ggcyto/R/scales_logicle.R ggcyto/R/stat_position.R ggcyto/R/utility.R
ggcyto/README.Rmd
ggcyto/README.md
ggcyto/README_files
ggcyto/README_files/figure-html
ggcyto/README_files/figure-html/unnamed-chunk-3-1.png
ggcyto/README_files/figure-html/unnamed-chunk-3-2.png
ggcyto/README_files/figure-html/unnamed-chunk-3-3.png
ggcyto/README_files/figure-html/unnamed-chunk-3-4.png
ggcyto/README_files/figure-html/unnamed-chunk-4-1.png
ggcyto/README_files/figure-html/unnamed-chunk-5-1.png
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ggcyto/README_files/figure-html/unnamed-chunk-6-2.png
ggcyto/README_files/figure-html/unnamed-chunk-6-3.png
ggcyto/build
ggcyto/build/partial.rdb
ggcyto/build/vignette.rds
ggcyto/inst
ggcyto/inst/NEWS
ggcyto/inst/doc
ggcyto/inst/doc/Top_features_of_ggcyto.R
ggcyto/inst/doc/Top_features_of_ggcyto.Rmd
ggcyto/inst/doc/Top_features_of_ggcyto.html
ggcyto/inst/doc/autoplot.R
ggcyto/inst/doc/autoplot.Rmd
ggcyto/inst/doc/autoplot.html
ggcyto/inst/doc/ggcyto.GatingSet.R
ggcyto/inst/doc/ggcyto.GatingSet.Rmd
ggcyto/inst/doc/ggcyto.GatingSet.html
ggcyto/inst/doc/ggcyto.flowSet.R
ggcyto/inst/doc/ggcyto.flowSet.Rmd
ggcyto/inst/doc/ggcyto.flowSet.html
ggcyto/man
ggcyto/man/as.ggplot.Rd ggcyto/man/autoplot.Rd ggcyto/man/axis_x_inverse_trans.Rd ggcyto/man/compute_stats.Rd ggcyto/man/fortify.ellipsoidGate.Rd ggcyto/man/fortify.filterList.Rd ggcyto/man/fortify.flowSet.Rd ggcyto/man/fortify.polygonGate.Rd ggcyto/man/fortify.rectangleGate.Rd ggcyto/man/fortify_fs.Rd ggcyto/man/geom_gate.Rd
ggcyto/man/geom_hvline.Rd
ggcyto/man/geom_overlay.Rd ggcyto/man/geom_stats.Rd ggcyto/man/getFlowFrame.Rd ggcyto/man/ggcyto.GatingSet.Rd ggcyto/man/ggcyto.Rd ggcyto/man/ggcyto.flowSet.Rd ggcyto/man/ggcyto_GatingSet_add.Rd ggcyto/man/ggcyto_arrange.Rd ggcyto/man/ggcyto_flowSet_add.Rd ggcyto/man/ggcyto_par_default.Rd ggcyto/man/ggcyto_par_set.Rd ggcyto/man/is.ggcyto.Rd ggcyto/man/is.ggcyto_flowSet.Rd ggcyto/man/is.ggcyto_par.Rd ggcyto/man/labs_cyto.Rd ggcyto/man/marginalFilter.Rd ggcyto/man/plus-.ggcyto_GatingLayout.Rd ggcyto/man/print.ggcyto.Rd ggcyto/man/print.ggcyto_GatingLayout.Rd ggcyto/man/scale_x_flowJo_biexp.Rd ggcyto/man/scale_x_flowJo_fasinh.Rd ggcyto/man/scale_x_logicle.Rd ggcyto/man/stat_position.Rd
ggcyto/vignettes
ggcyto/vignettes/Top_features_of_ggcyto.Rmd
ggcyto/vignettes/Top_features_of_ggcyto_files
ggcyto/vignettes/Top_features_of_ggcyto_files/figure-html
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ggcyto/vignettes/advanced
ggcyto/vignettes/advanced/ggplot.flowSet.1d.Rmd
ggcyto/vignettes/advanced/ggplot.flowSet.1d.html
ggcyto/vignettes/advanced/ggplot.flowSet.1d.md
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files
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ggcyto/vignettes/advanced/ggplot.flowSet.2d.Rmd
ggcyto/vignettes/advanced/ggplot.flowSet.2d.html
ggcyto/vignettes/advanced/ggplot.flowSet.2d.md
ggcyto/vignettes/advanced/ggplot.flowSet.2d_files
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ggcyto/vignettes/advanced/ggplot.flowSet.gate.Rmd
ggcyto/vignettes/advanced/ggplot.flowSet.gate.html
ggcyto/vignettes/advanced/ggplot.flowSet.gate.md
ggcyto/vignettes/advanced/ggplot.flowSet.gate_files
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ggcyto/vignettes/advanced/ggplot.flowSet.overlay.Rmd
ggcyto/vignettes/advanced/ggplot.flowSet.overlay.html
ggcyto/vignettes/advanced/ggplot.flowSet.overlay.md
ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files
ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files/figure-html
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ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-3.png
ggcyto/vignettes/autoplot.Rmd
ggcyto/vignettes/autoplot_files
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ggcyto/vignettes/ggcyto.GatingSet.Rmd
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ggcyto/vignettes/ggcyto.flowSet.Rmd
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ggcyto/vignettes/ggcyto.html

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