flowPlots: flowPlots: analysis plots and data class for gated flow cytometry data
Version 1.24.0

Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.

Browse man pages Browse package API and functions Browse package files

AuthorN. Hawkins, S. Self
Bioconductor views CellBasedAssays DataRepresentation FlowCytometry Visualization
Date of publicationNone
MaintainerN. Hawkins <hawkins@fhcrc.org>
LicenseArtistic-2.0
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowPlots")

Man pages

adultsNeonates: The adultsNeonates example data set of "stacked" data.
computeMarginalData-methods: Method computeMarginalData from Class "StackedData"
computeMarkers-methods: Method computeMarkers from Class "StackedData"
computePFDData-methods: Method computePFDData from Class "StackedData"
computePFDGroupStatsList: Compute Group Stats on PFD Data to Be Used In a Legend
computePFDPartsData-methods: Method computePFDPartsData from Class "StackedData"
computeProfileData-methods: Method computeProfileData from Class "StackedData"
GroupListBoxplot: A Boxplot Function With Embedded Statistical Tests for...
legendPFDStatsGroupNames: Create Group Names With Embedded Stats to Use in a Plot...
makeBarplotData: Prepare Profile Data for a Call to Barplot()
makeDataList: Prepare Data in a Data Frame for a Call to GroupListBoxplot()
makeTernaryData: Prepare PFD Data for a Call to ternaryplot()
marginalData-methods: Method marginalData from Class "StackedData"
marginalDF: An example of marginalData
markerMatrix: An example of the markers data.
markers-methods: Method markers from Class "StackedData"
pfdData-methods: Method pfdData from Class "StackedData"
pfdDF: An example of pfdData
pfdPartsData-methods: Method pfdPartsData from Class "StackedData"
pfdPartsList: An example of pfdPartsData
profileData-methods: Method profileData from Class "StackedData"
profileDF: An example of profileData
readStackedData-methods: Method readStackedData from Class "StackedData"
StackedData-class: Class "StackedData"
stackedData-methods: Method stackedData from Class "StackedData"

Functions

GroupListBoxplot Man page Source code
StackedData Man page
StackedData-class Man page
adultsNeonates Man page
assignCategoryGroups Source code
computeMarginalData Man page
computeMarginalData,StackedData,character,character,character,ch Man page
computeMarginalData-methods Man page
computeMarkers Man page
computeMarkers,character,logical-method Man page
computeMarkers-methods Man page
computePFDData Man page
computePFDData,StackedData,character,character,character,charact Man page
computePFDData-methods Man page
computePFDGroupStatsList Man page Source code
computePFDPartsData Man page
computePFDPartsData,StackedData,character,character,character,ch Man page
computePFDPartsData-methods Man page
computeProfileData Man page
computeProfileData,StackedData,character,character,character,cha Man page
computeProfileData-methods Man page
computeYmaxBoxplot Source code
createSummaryData Source code
get2GroupPValues Source code
getMaxOfListData Source code
getMinOfListData Source code
getMultiGroupPValues Source code
getNs Source code
getNsOfListData Source code
getPValueLabels Source code
getXAxisAtPoints Source code
legendPFDStatsGroupNames Man page Source code
makeBarplotData Man page Source code
makeDataList Man page Source code
makeTernaryData Man page Source code
marginalDF Man page
marginalData Man page
marginalData,StackedData-method Man page
marginalData-methods Man page
marginalData<- Man page
marginalData<-,StackedData-method Man page
marginalData<--methods Man page
markerMatrix Man page
markerPercentPositive Source code
markerPercentPositiveAnyMarker Source code
markers Man page
markers,StackedData-method Man page
markers-methods Man page
markers<- Man page
markers<-,StackedData-method Man page
markers<--methods Man page
numericFactor Source code
pfd Source code
pfdDF Man page
pfdData Man page
pfdData,StackedData-method Man page
pfdData-methods Man page
pfdData<- Man page
pfdData<-,StackedData-method Man page
pfdData<--methods Man page
pfdParts Source code
pfdPartsData Man page
pfdPartsData,StackedData-method Man page
pfdPartsData-methods Man page
pfdPartsData<- Man page
pfdPartsData<-,StackedData-method Man page
pfdPartsData<--methods Man page
pfdPartsList Man page
profileDF Man page
profileData Man page
profileData,StackedData-method Man page
profileData-methods Man page
profileData<- Man page
profileData<-,StackedData-method Man page
profileData<--methods Man page
profilePercents Source code
readStackedData Man page
readStackedData,character-method Man page
stackedData Man page
stackedData,StackedData-method Man page
stackedData-methods Man page
stackedData<- Man page
stackedData<-,StackedData-method Man page
stackedData<--methods Man page
weightedPFDMean Source code

Files

DESCRIPTION
INDEX
NAMESPACE
R
R/class.StackedData.HelperFcns.R
R/class.StackedData.R
R/pkg.GroupListBoxplot.R
R/pkg.HelperFcns.R
R/pkg.HelperPlotFcns.R
build
build/vignette.rds
data
data/adultsNeonates.rda
data/marginalDF.rda
data/markerMatrix.rda
data/pfdDF.rda
data/pfdPartsList.rda
data/profileDF.rda
inst
inst/doc
inst/doc/flowPlots.R
inst/doc/flowPlots.Rnw
inst/doc/flowPlots.pdf
inst/extdata
inst/extdata/adultsNeonates.csv
man
man/GroupListBoxplot.Rd
man/StackedData-class.Rd
man/adultsNeonates.Rd
man/computeMarginalData-methods.Rd
man/computeMarkers-methods.Rd
man/computePFDData-methods.Rd
man/computePFDGroupStatsList.Rd
man/computePFDPartsData-methods.Rd
man/computeProfileData-methods.Rd
man/legendPFDStatsGroupNames.Rd
man/makeBarplotData.Rd
man/makeDataList.Rd
man/makeTernaryData.Rd
man/marginalDF.Rd
man/marginalData-methods.Rd
man/markerMatrix.Rd
man/markers-methods.Rd
man/pfdDF.Rd
man/pfdData-methods.Rd
man/pfdPartsData-methods.Rd
man/pfdPartsList.Rd
man/profileDF.Rd
man/profileData-methods.Rd
man/readStackedData-methods.Rd
man/stackedData-methods.Rd
vignettes
vignettes/flowPlots.Rnw
vignettes/theRefs.bib
flowPlots documentation built on May 20, 2017, 10:38 p.m.