plot: Plot a summary of an FIA experiment.
In adelabriere/proFIA: Preprocessing of FIA-HRMS data

Description Usage Arguments Value Examples

Plot a summary of an FIA acquisition. This summary aims to provides an overview of the FIA acquisition and the processinf of FIA acquisition. It includes the following graphs :

Barplot A barplot giving the number of peak detected in each sample. The number of shifted peak is indicated, which can indicate wrong FIA-acquisition, as well as the number of peak badly with a low correlation with the injection peak, which can indicate a strong matrix effect.
Injection_Peaks A representation of all the injection peaks of the acquisition, a greatly different peak in th einjection may indicate an issue with the injection, or a problem of regression. If the peaks seems all different, try to use proFIAset with the f paramter on TIC, to avoid regression.
Density A density plot of the m/z of all the features found. A missing interval at the end of the mz range may indicate a too low ppm parameter, while a missing interval at the beginning of the mz range may indicate a too low dmz parameter.
PCA A PCA plot to obtain a quick diagnostic of the data. The PCA plot is supposed to be different before and after imputation.

1 2	## S4 method for signature 'proFIAset,ANY' plot(x, type = c("sample", "class"), ...)

`x`	A proFIAset object.
`type`	Shall the plotting be done by sample or by class for the barplot ?
`...`	Not used at the moment.

Nothing

if(require("plasFIA")){
   data(plasSet)
   
   
   ####Diagnostic plot after imputation
   plot(plasSet)
   
   ####The same plot by classes.
   plot(plasSet,type="class")
   
   ####Diagnostic plot before imputation
   plasSet <- makeDataMatrix(plasSet)
  plot(plasSet)

}