plotMetricTibble: Helper function for plotMetric

View source: R/function_visualizations.R

plotMetricTibbleR Documentation

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 'rtDuration' only the column 'rtDuration' will be selected), the 'name' column will include the 'metric' ('rtDuration').

Value

'tibble'

Author(s)

Thomas Naake, thomasnaake@googlemail.com

Examples

library(msdata)

## 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 mse object
sps <- Spectra(fls, backend = MsBackendMzR())

## define the quality metrics to be calculated
metrics <- c("areaUnderTic", "rtDuration", "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 <- calculateMetricsFromSpectra(spectra = sps, metrics = metrics, 
    msLevel = 1, relativeTo = "Q1", change = "jump")
rownames(qc) <- c("Sample 1", "Sample 2")
plotMetricTibble(qc, metric = "areaUnderTic")

tnaake/MsQuality documentation built on Dec. 1, 2022, 10:01 p.m.