ggcyto: Visualize Cytometry data with ggplot
Version 1.4.0

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
Bioconductor views CellBasedAssays FlowCytometry Infrastructure Visualization
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.4.0
URL https://github.com/RGLab/ggcyto/issues
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ggcyto")

Getting started

README.md
ggcyto : Visualize `Cytometry` data with `ggplot`
Quick plot for cytometry data
Visualize flowSet with ggcyto
Visualize GatingSet with ggcyto

Popular man pages

autoplot: Plot fluorescence intensity in one or two dimension.
geom_gate: add a flowCore gate layer
getFlowFrame: extract flowFrame data structure from the given R object
ggcyto: Create a new ggcyto plot
ggcyto.flowSet: Create a new ggcyto plot from a flowSet
scale_x_flowJo_biexp: flowJo biexponential scale
scale_x_logicle: flowJo inverse hyperbolic sine scale
See all...

All man pages Function index File listing

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

+,ggcyto_GatingLayout,ANY-method Man page
+,ggcyto_GatingSet,ANY-method Man page
+,ggcyto_flowSet,ANY-method Man page
+.ggcyto_GatingLayout Man page
+.ggcyto_GatingSet Man page
+.ggcyto_flowSet Man page
add_ggcyto Source code
add_ggcyto_gs Source code
add_par Source code
as.GatingSet Source code
as.ggplot Man page Source code
autoplot.GatingHierarchy Man page Source code
autoplot.GatingSet Man page Source code
autoplot.GatingSetList Man page Source code
autoplot.flowFrame Man page Source code
autoplot.flowSet Man page Source code
autoplot.ncdfFlowList Man page Source code
axis_x_inverse_trans Man page Source code
axis_y_inverse_trans Man page Source code
compute_stats Man page Source code
density_fr_all Source code
do_loop Source code
element_tree Source code
filterList2dataframe Source code
fixInf Source code
fortify Man page
fortify.GatingSet Man page Source code
fortify.GatingSetList Man page Source code
fortify.ellipsoidGate Man page Source code
fortify.filterList Man page Source code
fortify.flowFrame Man page Source code
fortify.flowSet Man page Source code
fortify.ncdfFlowList Man page Source code
fortify.polygonGate Man page Source code
fortify.rectangleGate Man page Source code
fortify_fs Man page Source code
fortify_fs.GatingSet Man page Source code
fortify_fs.GatingSetList Man page Source code
fortify_fs.default Man page Source code
fortify_fs.flowFrame Man page Source code
fortify_fs.flowSet Man page Source code
fr2dt Source code
fs2dt Source code
fsdply Source code
gate2dataframe Source code
geom_gate Man page Source code
geom_gate.character Man page Source code
geom_gate.default Man page Source code
geom_gate.ellipsoidGate Man page Source code
geom_gate.filterList Man page Source code
geom_gate.filters Man page Source code
geom_gate.filtersList Man page Source code
geom_gate.list Man page Source code
geom_gate.logical Man page Source code
geom_gate.logicalFilterResult Man page Source code
geom_gate.polygonGate Man page Source code
geom_gate.rectangleGate Man page Source code
geom_gate_filterList Source code
geom_gate_polygonGate Source code
geom_gate_rectangleGate Source code
geom_hvline Source code
geom_overlay Man page Source code
geom_overlay.character Man page Source code
geom_overlay.default Man page Source code
geom_overlay.flowFrame Man page Source code
geom_overlay.flowSet Man page Source code
geom_overlay.ncdfFlowList Man page Source code
geom_stats Man page Source code
getChildren_by_projection Source code
getFlowFrame Man page Source code
getFlowFrame.GatingHierarchy Man page Source code
getFlowFrame.GatingSet Man page Source code
getFlowFrame.GatingSetList Man page Source code
getFlowFrame.flowSet Man page Source code
getFlowFrame.ncdfFlowList Man page Source code
ggcyto Man page Source code
ggcyto-class Man page
ggcyto.GatingHierarchy Man page Source code
ggcyto.GatingSet Man page Source code
ggcyto.GatingSetList Man page Source code
ggcyto.default Man page Source code
ggcyto.flowSet Man page Source code
ggcyto.ncdfFlowList Man page Source code
ggcyto_GatingLayout-class Man page
ggcyto_GatingSet-class Man page
ggcyto_arrange Man page Source code
ggcyto_flowSet-class Man page
ggcyto_par_default Man page Source code
ggcyto_par_set Man page Source code
ggproto.copy Source code
is.geom_gate_filterList Source code
is.ggcyto Man page Source code
is.ggcyto_flowSet Man page Source code
is.ggcyto_par Man page Source code
labs_cyto Man page Source code
ldply Source code
marginalFilter Man page Source code
my_compute_aesthetics Source code
pd2dt Source code
plot.ggcyto Man page
print,ggcyto-method Man page
print.ggcyto Man page Source code
print.ggcyto_GatingLayout Man page Source code
range_intersect Source code
scale_x_flowJo_biexp Man page Source code
scale_x_flowJo_fasinh Man page Source code
scale_x_logicle Man page Source code
scale_y_flowJo_biexp Man page Source code
scale_y_flowJo_fasinh Man page Source code
scale_y_logicle Man page Source code
show,ggcyto-method Man page
show,ggcyto_GatingLayout-method Man page
show.ggcyto Man page Source code
show.ggcyto_GatingLayout Man page Source code
stat_MFI Source code
stat_count Source code
stat_percent Source code
stat_position Man page Source code
stat_position.filter Man page Source code
stat_position.filterList Man page Source code
stat_position.list Man page Source code
stat_position_filter Source code
validate_element Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/autoplot.R
R/axis_inverse_trans.R
R/compute_stats.R
R/fortify.R
R/fortify_fs.R
R/geom_gate.R
R/geom_hvline.R
R/geom_overlay.R
R/geom_stats.R
R/getFlowFrame.R
R/ggcyto.R
R/ggcyto_GatingLayout.R
R/ggcyto_GatingSet.R
R/ggcyto_flowSet.R
R/ggcyto_par.R
R/labs.R
R/scales_flowJo_biexp.R
R/scales_flowJo_fasinh.R
R/scales_logicle.R
R/stat_position.R
R/utility.R
README.Rmd
README.md
README_files
README_files/figure-html
README_files/figure-html/unnamed-chunk-3-1.png
README_files/figure-html/unnamed-chunk-3-2.png
README_files/figure-html/unnamed-chunk-3-3.png
README_files/figure-html/unnamed-chunk-3-4.png
README_files/figure-html/unnamed-chunk-4-1.png
README_files/figure-html/unnamed-chunk-5-1.png
README_files/figure-html/unnamed-chunk-5-2.png
README_files/figure-html/unnamed-chunk-5-3.png
README_files/figure-html/unnamed-chunk-6-1.png
README_files/figure-html/unnamed-chunk-6-2.png
README_files/figure-html/unnamed-chunk-6-3.png
build
build/partial.rdb
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/Top_features_of_ggcyto.R
inst/doc/Top_features_of_ggcyto.Rmd
inst/doc/Top_features_of_ggcyto.html
inst/doc/autoplot.R
inst/doc/autoplot.Rmd
inst/doc/autoplot.html
inst/doc/ggcyto.GatingSet.R
inst/doc/ggcyto.GatingSet.Rmd
inst/doc/ggcyto.GatingSet.html
inst/doc/ggcyto.flowSet.R
inst/doc/ggcyto.flowSet.Rmd
inst/doc/ggcyto.flowSet.html
man
man/as.ggplot.Rd
man/autoplot.Rd
man/axis_x_inverse_trans.Rd
man/compute_stats.Rd
man/fortify.ellipsoidGate.Rd
man/fortify.filterList.Rd
man/fortify.flowSet.Rd
man/fortify.polygonGate.Rd
man/fortify.rectangleGate.Rd
man/fortify_fs.Rd
man/geom_gate.Rd
man/geom_hvline.Rd
man/geom_overlay.Rd
man/geom_stats.Rd
man/getFlowFrame.Rd
man/ggcyto.GatingSet.Rd
man/ggcyto.Rd
man/ggcyto.flowSet.Rd
man/ggcyto_GatingSet_add.Rd
man/ggcyto_arrange.Rd
man/ggcyto_flowSet_add.Rd
man/ggcyto_par_default.Rd
man/ggcyto_par_set.Rd
man/is.ggcyto.Rd
man/is.ggcyto_flowSet.Rd
man/is.ggcyto_par.Rd
man/labs_cyto.Rd
man/marginalFilter.Rd
man/plus-.ggcyto_GatingLayout.Rd
man/print.ggcyto.Rd
man/print.ggcyto_GatingLayout.Rd
man/scale_x_flowJo_biexp.Rd
man/scale_x_flowJo_fasinh.Rd
man/scale_x_logicle.Rd
man/stat_position.Rd
vignettes
vignettes/Top_features_of_ggcyto.Rmd
vignettes/Top_features_of_ggcyto_files
vignettes/Top_features_of_ggcyto_files/figure-html
vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-10-1.png
vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-10-2.png
vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-11-1.png
vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-11-2.png
vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-12-1.png
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vignettes/Top_features_of_ggcyto_files/figure-html/unnamed-chunk-9-4.png
vignettes/advanced
vignettes/advanced/ggplot.flowSet.1d.Rmd
vignettes/advanced/ggplot.flowSet.1d.html
vignettes/advanced/ggplot.flowSet.1d.md
vignettes/advanced/ggplot.flowSet.1d_files
vignettes/advanced/ggplot.flowSet.1d_files/figure-html
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vignettes/advanced/ggplot.flowSet.1d_files/figure-html/unnamed-chunk-3-9.png
vignettes/advanced/ggplot.flowSet.2d.Rmd
vignettes/advanced/ggplot.flowSet.2d.html
vignettes/advanced/ggplot.flowSet.2d.md
vignettes/advanced/ggplot.flowSet.2d_files
vignettes/advanced/ggplot.flowSet.2d_files/figure-html
vignettes/advanced/ggplot.flowSet.2d_files/figure-html/unnamed-chunk-3-1.png
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vignettes/advanced/ggplot.flowSet.2d_files/figure-html/unnamed-chunk-3-9.png
vignettes/advanced/ggplot.flowSet.gate.Rmd
vignettes/advanced/ggplot.flowSet.gate.html
vignettes/advanced/ggplot.flowSet.gate.md
vignettes/advanced/ggplot.flowSet.gate_files
vignettes/advanced/ggplot.flowSet.gate_files/figure-html
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vignettes/advanced/ggplot.flowSet.gate_files/figure-html/unnamed-chunk-3-9.png
vignettes/advanced/ggplot.flowSet.overlay.Rmd
vignettes/advanced/ggplot.flowSet.overlay.html
vignettes/advanced/ggplot.flowSet.overlay.md
vignettes/advanced/ggplot.flowSet.overlay_files
vignettes/advanced/ggplot.flowSet.overlay_files/figure-html
vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-1.png
vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-2.png
vignettes/advanced/ggplot.flowSet.overlay_files/figure-html/unnamed-chunk-3-3.png
vignettes/autoplot.Rmd
vignettes/autoplot_files
vignettes/autoplot_files/figure-html
vignettes/autoplot_files/figure-html/unnamed-chunk-3-1.png
vignettes/autoplot_files/figure-html/unnamed-chunk-3-2.png
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vignettes/autoplot_files/figure-html/unnamed-chunk-8-1.png
vignettes/autoplot_files/figure-html/unnamed-chunk-9-1.png
vignettes/ggcyto.GatingSet.Rmd
vignettes/ggcyto.GatingSet_files
vignettes/ggcyto.GatingSet_files/figure-html
vignettes/ggcyto.GatingSet_files/figure-html/unnamed-chunk-10-1.png
vignettes/ggcyto.GatingSet_files/figure-html/unnamed-chunk-11-1.png
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vignettes/ggcyto.GatingSet_files/figure-html/unnamed-chunk-9-1.png
vignettes/ggcyto.flowSet.Rmd
vignettes/ggcyto.flowSet_files
vignettes/ggcyto.flowSet_files/figure-html
vignettes/ggcyto.flowSet_files/figure-html/unnamed-chunk-10-1.png
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ggcyto documentation built on May 20, 2017, 10:18 p.m.

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