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.
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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(plateCore)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Attaching package: 'latticeExtra'
The following object is masked from 'package:flowViz':
ecdfplot
sROC 0.1-2 loaded
No methods found in "flowStats" for requests: %on%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/plateCore/mfiPlot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mfiPlot
> ### Title: mfiPlot
> ### Aliases: mfiPlot mfiPlot-method mfiPlot,flowPlate-method
> ### Keywords: methods
>
> ### ** 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)
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.