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