PeacoQCHeatmap: Make overview heatmap of quality control analysis

In saeyslab/PeacoQC: Peak-based selection of high quality cytometry data

Make overview heatmap of quality control analysis

Description

PeacoQCHeatmap will make a heatmap to display all the results generated by PeacoQC. It will include the percentages of measurements that are removed in total, by the IT method and by the MAD method. It will also show the parameters that were used during the quality control.

Usage

PeacoQCHeatmap(report_location, show_values=TRUE, show_row_names=TRUE,
latest_tests=FALSE, title="PeacoQC report", ...)

Arguments

report_location	The path to the PeacoQC report generated by PeacoQC.
show_values	If set to TRUE, the percentages of removed values will be displayed on the heatmap. Default is TRUE.
show_row_names	If set to FALSE, the filenames will not be displayed on the heatmap. Default is TRUE.
latest_tests	If this is set to TRUE, only the latest quality control run will be displayed in the heatmap. Default is FALSE.
title	The title that should be given to the heatmap. Default is "PeacoQC_report".
...	Extra parameters to be given to the Heatmap function (eg. row_split)

Value

This function returns nothing but generates a heatmap that can be saved as pdf or png

Examples

# Find path to PeacoQC report
location <- system.file("extdata", "PeacoQC_report.txt", package="PeacoQC")

# Make heatmap overview of quality control run
PeacoQCHeatmap(report_location=location)

# Make heatmap with only the runs of the last test
PeacoQCHeatmap(report_location=location, latest_tests=TRUE)

# Make heatmap with row annotation
PeacoQCHeatmap(report_location=location,
              row_split=c(rep("r1",7), rep("r2", 55)))

saeyslab/PeacoQC documentation built on Aug. 24, 2023, 8:11 a.m.