plotMetricTibble: Helper function for plotMetric

In tnaake/MsQuality: MsQuality - Quality metric calculation from Spectra and MsExperiment objects

Helper function for plotMetric

Description

The function plotMetricTibble is a helper function for the function plotMetric. It returns a tibble in long format that is interpretable by ggplot2.

Usage

plotMetricTibble(qc, metric)

Arguments

qc	data.frame
metric	character

Details

plotMetricRibble will select all columns that start with metric. The different levels in the name column in the returned tibble correspond to the columns that were selected and do not contain the metric prefix. In case there is no additional specification (e.g. for the metric chromatographyDuration only the column chromatographyDuration will be selected), the name column will include the metric (chromatographyDuration).

Value

tibble

Author(s)

Thomas Naake, [e-mail]

Examples

library(msdata)
library(MsExperiment)
library(S4Vectors)
msexp <- MsExperiment()
sd <- DataFrame(sample_id = c("QC1", "QC2"),
    sample_name = c("QC Pool", "QC Pool"), injection_idx = c(1, 3))
sampleData(msexp) <- sd

## define file names containing spectra data for the samples and
## add them, along with other arbitrary files to the experiment
fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
experimentFiles(msexp) <- MsExperimentFiles(
    mzML_files = fls,
    annotations = "internal_standards.txt")
## link samples to data files: first sample to first file in "mzML_files",
## second sample to second file in "mzML_files"
msexp <- linkSampleData(msexp, with = "experimentFiles.mzML_files",
    sampleIndex = c(1, 2), withIndex = c(1, 2))
msexp <- linkSampleData(msexp, with = "experimentFiles.annotations",
    sampleIndex = c(1, 2), withIndex = c(1, 1))

library(Spectra)
## import the data and add it to the mse object
spectra(msexp) <- Spectra(fls, backend = MsBackendMzR())

## define the quality metrics to be calculated
metrics <- c("areaUnderTic", "chromatographyDuration", "msSignal10xChange")

## calculate the metrics
## additional parameters passed to the quality metrics functions
## (msLevel is an argument of areaUnderTic and msSignal10xChange,
## relativeTo is an argument of msSignal10xChange)
qc <- calculateMetricsFromMsExperiment(msexp = msexp, metrics = metrics, 
    msLevel = 1, relativeTo = "Q1", change = "jump")
rownames(qc) <- c("Sample 1", "Sample 2")
plotMetricTibble(qc, metric = "areaUnderTic")

tnaake/MsQuality documentation built on Feb. 25, 2024, 7:32 p.m.