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.

Author
Mike Jiang
Date of publication
None
Maintainer
Mike Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
1.2.1
URLs

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_hvline
Vertical or horizontal line.
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
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
ggcyto/README_files/figure-html/unnamed-chunk-5-2.png
ggcyto/README_files/figure-html/unnamed-chunk-5-3.png
ggcyto/README_files/figure-html/unnamed-chunk-6-1.png
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
ggcyto/vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-10-1.png
ggcyto/vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-10-2.png
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ggcyto/vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-12-1.png
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ggcyto/vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-9-4.png
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
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-1.png
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ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-11.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-12.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-13.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-14.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-15.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-16.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-17.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-2.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-3.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-4.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-5.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-6.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-7.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-8.png
ggcyto/vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-9.png
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
ggcyto/vignettes/advanced/ggplot.flowSet.2d_files/figure-html
ggcyto/vignettes/advanced/ggplot.flowSet.2d_files/figure-html/unnamed-chunk-3-1.png
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ggcyto/vignettes/advanced/ggplot.flowSet.2d_files/figure-html/unnamed-chunk-3-9.png
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
ggcyto/vignettes/advanced/ggplot.flowSet.gate_files/figure-html
ggcyto/vignettes/advanced/ggplot.flowSet.gate_files/figure-html/unnamed-chunk-3-1.png
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ggcyto/vignettes/advanced/ggplot.flowSet.gate_files/figure-html/unnamed-chunk-3-9.png
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
ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-1.png
ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-2.png
ggcyto/vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-3.png
ggcyto/vignettes/autoplot.Rmd
ggcyto/vignettes/autoplot_files
ggcyto/vignettes/autoplot_files/figure-html
ggcyto/vignettes/autoplot_files/figure-html/unnamed-chunk-3-1.png
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ggcyto/vignettes/ggcyto.GatingSet.Rmd
ggcyto/vignettes/ggcyto.GatingSet_files
ggcyto/vignettes/ggcyto.GatingSet_files/figure-html
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ggcyto/vignettes/ggcyto.flowSet.Rmd
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