PTXQC (version 1.0.4)

qcMetric-class: Class which can compute plots (usually for a single metric).

Description

Reference class which is instanciated with a metric description and a worker function (at initialization time, i.e. in the package) and can produce plots (at runtime, when data is provided) using setData().

Fields

helpText

Description (lengthy) of the metric and plot elements

workerFcn

Function which generates a result (usually plots). Data is provided using setData().

plots

List of plots (after setData() was called)

qcScores

[placeholder] Data.frame of scores from a qcMetric (computed within workerFcn())

qcCat

[placeholder] QC category (LC, MS, or prep)

qcName

[placeholder] Name of the qcScore in the heatmap

orderNr

[placeholder] column index during heatmap generation and for the general order of plots

Examples

# NOT RUN {
require(ggplot2)
dd = data.frame(x=1:10, y=11:20)
a = qcMetric$new(helpText="small help text", 
                 ## arbitrary arguments, matched during setData()
                 workerFcn=function(.self, data, gtit)
                 {
                   ## usually some code here to produce ggplots
                   pl = lapply(1:2, function(xx) {
                       ggplot(data) +
                         geom_point(aes(x=x*xx,y=y)) +
                         ggtitle(gtit)
                     })
                   return(list(plots = pl))
                 }, 
                 qcCat="LC", 
                 qcName="MS/MS Peak shape", 
                 orderNr = 30)
## test some output
a$setData(dd, "my title")
a$plots  ## the raw plots
a$getPlots(TRUE) ## same as above
a$getPlots(FALSE) ## plots without title
a$getTitles()  ## get the titles of the all plots
a$helpText
a$qcName



# }