DecisionMap: A function to create heatmaps to compare performance with...

Description Usage Arguments Value Examples

View source: R/DecisionMap.R

Description

A function to create heatmaps to compare performance with user defined performance criteria

Usage

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DecisionMap(data = NULL, method = "XmR", peptideThresholdRed = 0.7,
  peptideThresholdYellow = 0.5, L = 1, U = 5, type = "mean",
  title = "heatmap plot", listMean = NULL, listSD = NULL)

Arguments

data

Comma-separated (*.csv), QC file format. It should contain a Precursor column and the metrics columns.

method

It is either "CUSUM" or "XmR"

peptideThresholdRed

Is a threshold that marks percentage of peptides above it red on the heatmap. Defaults to 0.7

peptideThresholdYellow

Is a threshold that marks percentage of peptides above it and below the peptideThresholdRed, yellow on the heatmap. Defaults to 0.5

L

Lower bound of the giude set. Defaults to 1

U

Upper bound of the guide set. Defaults to 5

type

can take two values, "mean" or "dispersion". Defaults to "mean"

title

the title of the plot. Defaults to "heatmap plot"

listMean

List of the means for the metrics. If you don't know the means leave it as NULL and they will be calculated automatically by using L and U. The default is NULL.

listSD

List of the standard deviations for the metrics. If you don't know the standard deviations leave it as NULL and they will be calculated automatically by using L and U. The default is NULL.

Value

A heatmap to aggregate results per metric generated from heatmap.DataFrame data frame.

Examples

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# First process the data to make sure it's ready to use
sampleData <- DataProcess(S9Site54)
head(sampleData)
# Draw Decision maker plot
DecisionMap(data = sampleData, method = "CUSUM")
DecisionMap(data = sampleData, method = "CUSUM", type = "variability")
DecisionMap(data = sampleData, method = "XmR")
DecisionMap(data = sampleData, method = "XmR", type = "variability")
DecisionMap(data = sampleData, method = "CUSUM", type = "mean",
              listMean = list("BestRetentionTime" = 27.78,
                              "TotalArea" = 35097129,
                              "MaxFWHM" = 0.28,
                              "Peak Assymetry" = 0.98),
              listSD = list("BestRetentionTime" = 8.19,
                            "TotalArea" = 34132861,
                            "MaxFWHM" = 0.054,
                            "Peak Assymetry" = 0.002)
                 )

eralpdogu/MSstatsQC documentation built on Sept. 23, 2018, 5:19 a.m.