The simsMVA app is developed on Matlab 2016b and, alongside with in-house developed functions, makes use of the Statistics and Machine Learning and the Image Processing toolboxes. The main window will contain a menu bar with three options: “New tab”, “Theme” and “Help”. The “New tab” menu contains four different options: “Spectra”, “Images”, “Profiles” and “3D”. Every time one of these options are selected, a new tab is created under a name that the user is prompted to give. The “Theme” menu contains a set of different colour schemes that can be applied to the GUI. A detailed description of each feature present in each kind of tab is given in Table 1.
A Spectra tab is shown in Figure 5. It contains a java-based table (Copyright (c) 2015, Yair Altman. All rights reserved) with all loaded data: peak areas of different samples and their associated mass and labels. The first column contains tick boxes that allow the user to unselect specific variables prior to multivariate analysis. The figures on the left hand side show a plot of the average peak list for all samples. The upper image will always show the original data and the bottom figure will show the pre-processed data. The figure on the bottom left will contain a scatter plot where the user can select which peak areas to plot against each other. A Profiles tab is shown Figure 6. It contains a table on the right hand side that allows the selection of which peak intensity profile to plot on the set of axis on the left hand side. An Images tab is shown in Figure 7. The image on the top left hand side will show the intensity maps for the selected ion. The two plots on the right hand side will show the intensity distribution of the peak list (after selected pre-processing) outside (top) and inside (bottom) of the region of interest determined by a red polygon on the left hand side map. The image on the bottom left will contain an RGB overlay of three different mass fragments maps selected by the user. A 3D tab is shown in Figure 8. The image on the top left side will show the intensity maps for the selected ion at the selected level. The two plots on the right hand side will show the intensity distribution of the peak list (after selected pre-processing) outside (top) and inside (bottom) of the region of interest determined by a red polygon on the left hand side map. The image on the bottom left will have a 3D map of intensities with a slice on the currently selected level.
Both images and 3D tabs will have the option of subsampling the data using low discrepancy which have been shown to generate, in much less time, results as good as if the whole dataset was processed [13–15].
Table 1: Detailed description of each feature present in each kind of tab.