I just wanted to inform you about an issue with the plotCompareMethodsAll() function. I wondered about the figures I got with the function, as it looked as if the intensity pie charts and peak pie charts were reversed. Therefore, I checked the code for the function here on Github and found that when the matrix is created for the plot "Intensity" and "Peak" are reversed. So indeed the Intensity pie charts actually show the Peak data and the Peak pie charts show the Intensity data.
I just wanted to inform you about an issue with the plotCompareMethodsAll() function. I wondered about the figures I got with the function, as it looked as if the intensity pie charts and peak pie charts were reversed. Therefore, I checked the code for the function here on Github and found that when the matrix is created for the plot "Intensity" and "Peak" are reversed. So indeed the Intensity pie charts actually show the Peak data and the Peak pie charts show the Intensity data.
Best, Jenny