plotMetric: Visualize a quality metric

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

Visualize a quality metric

Description

The function plotMetric visualizes the metric values per sample. The function accepts the output of calculateMetrics or, calculateMetricsFromSpectra, or calculateMetricsFromMsExperiment and a vector specifying the metric to display.

Usage

plotMetric(qc, metric = "areaUnderTic", plotly = TRUE)

Arguments

qc	matrix/data.frame
metric	character
plotly	logical(1)

Details

plotMetric 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

gg plotly

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)

library(Spectra)
## import the data and add it to the msexp 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")

## do the actual plotting
plotMetric(qc, metric = "areaUnderTic", plotly = TRUE)

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