mfiPlot-methods: mfiPlot

In plateCore: Statistical tools and data structures for plate-based flow cytometry

Description

A Quality Control plot that shows the MFI Ratio versus the percentage of positive cells in a flowPlate. The robust logistic regression is performed using gmlrob from the robustbase package.

Usage

mfiPlot(fp, thresh=2, Sample.Type="Test",Events="Percentage", ...)

Arguments

fp	A flowPlate.
thresh	Points more than "thresh" number of standard deviations away from the best fit line will be colored red.
Sample.Type	Type of sample to show on plot. Defaults to "Test"
Events	The robust logistic regression can be performed using either the percentage of events above the negative control gate ("Percentage") or the actual number of events above the gate ("Actual").
...	optional arguments to plot and points.

Value

Creates a plot where the x-axis is MFI Ratio and the y-axis is the percentage of cells above the negative control gate.

Author(s)

Errol Strain

Examples

library(plateCore)
data(plateCore)

## Get the lymphocytes
rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))
pbmcPlate <- Subset(pbmcPlate, rectGate)

# Create a flowPlate from the sample data in plateCore
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")

# Create a set of negative control gates and then apply them
fp <- setControlGates(fp,gateType="Negative.Control")
fp <- applyControlGates(fp,gateType="Negative.Control")

# Compute summary statistics
fp <- summaryStats(fp)

## Create an MFI plot
mfiPlot(fp,thresh=2.5,xlab="MFI Ratio (Test MFI / Isotype MFI)",xlim=c(0.1,250),
		ylab="Percentage of cells above the isotype gate",pch=23)

plateCore documentation built on May 6, 2019, 2:41 a.m.