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

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

# First process the data to make sure it's ready to use
sampleData <- DataProcess(S9Site54)
#> Your data is ready to go!
head(sampleData)
#>    AcquiredTime Precursor   Annotations MinStartTime MaxEndTime
#> 1 9/19/11 13:14 VLVLDTDYK Not Available        24.30      25.08
#> 2 9/19/11 14:45 VLVLDTDYK Not Available        24.36      25.17
#> 3 9/19/11 16:15 VLVLDTDYK Not Available        24.19      24.96
#> 4 9/19/11 17:46 VLVLDTDYK Not Available        24.22      25.02
#> 5 9/19/11 19:16 VLVLDTDYK Not Available        24.27      25.05
#> 6 9/19/11 20:47 VLVLDTDYK Not Available        24.42      25.22
#>   BestRetentionTime TotalArea MaxFWHM missing
#> 1             24.62 116034248    0.29       0
#> 2             24.70 127339240    0.31       0
#> 3             24.53 110745576    0.31       0
#> 4             24.59 130619640    0.31       0
#> 5             24.62 113469472    0.30       0
#> 6             24.76 120836432    0.30       0
# Draw Decision maker plot
DecisionMap(data = sampleData, method = "CUSUM")
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the MSstatsQC package.
#>   Please report the issue at
#>   <https://groups.google.com/forum/#!forum/msstatsqc>.
#> Warning: Use of `data$time` is discouraged.
#> ℹ Use `time` instead.
#> Warning: Use of `data$metric` is discouraged.
#> ℹ Use `metric` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.

DecisionMap(data = sampleData, method = "CUSUM", type = "variability")
#> Warning: Use of `data$time` is discouraged.
#> ℹ Use `time` instead.
#> Warning: Use of `data$metric` is discouraged.
#> ℹ Use `metric` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.

DecisionMap(data = sampleData, method = "XmR")
#> Warning: Use of `data$time` is discouraged.
#> ℹ Use `time` instead.
#> Warning: Use of `data$metric` is discouraged.
#> ℹ Use `metric` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.

DecisionMap(data = sampleData, method = "XmR", type = "variability")
#> Warning: Use of `data$time` is discouraged.
#> ℹ Use `time` instead.
#> Warning: Use of `data$metric` is discouraged.
#> ℹ Use `metric` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.
#> Warning: Use of `data$bin` is discouraged.
#> ℹ Use `bin` instead.