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
Version1.2.1
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...

Files in this package

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
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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
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ggcyto/vignettes/advanced/ggplot.flowSet.2d.Rmd
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