Up: Component summary Component

GatingSummary

Generate summay report table and heatmap.

Version 1.0
Bundle flowand
Categories FlowCytometry
Authors Ping Chen (ping.chen@helsinki.fi)
Requires R ; fields (R-package)
Source files component.xml GatingSummary.r
Usage Example with default values

Inputs

Name Type Mandatory Description
summaries CSVList Mandatory A directory with CSV files which contain summarised intensities for each cluster.
sampleAnnotation CSV Mandatory A CSV annotation file with columns 'File', 'Stimulus', 'Panel' and 'PatientID'.
panel CSV Mandatory A CSV file with columns 'Panel' and 'Antibody' contains antibodies measured in each panel. Antibodies measured in each pannel are comma-separated.
population CSVList Mandatory Automatically gated cell populations.

Outputs

Name Type Description
summaryResult CSVList Summary tables for each patient.
report Latex Visualization of summarised results.

Parameters

Name Type Default Description
NAcolor string "pink" Color to use for missing value (NA).
colorSchema string "greenred" The color schema for plotting. It can be one of 'greenred', 'redgreen', 'redblue', 'bluered', 'heatcolor', 'rainbow' or 'blackyellowwhite'.
pagebreak boolean true Tells if the result document should start with a page break.
rotate boolean false Rotate output table if there are too many columns.
scale float 0.6 A scaling factor for the figure.
targetPop string "Monocytes" A string specifies the target population name measured for each patient.
type string "median" A string specifies how to merge data in multiple populations. It can be 'median' or 'mean'.
width float 2 Width (inches) of each square in heatmap.

Test cases

Test case Parameters IN
summaries
IN
sampleAnnotation
IN
panel
IN
population
OUT
summaryResult
OUT
report
case1 properties summaries sampleAnnotation panel population summaryResult report

colorSchema=greenred

case2 (missing) summaries sampleAnnotation panel population summaryResult report
case3 properties summaries sampleAnnotation panel population summaryResult report

colorSchema=greenred,
targetPop=Granulocytes


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