plot,proFIAset,ANY-method {proFIA} | R Documentation

## Plot a summary of an FIA experiment.

### Description

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.

### Usage

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

### Arguments

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

### Value

Nothing

### Examples

    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)

    }

[Package proFIA version 1.18.0 Index]