Table 1.
Example format of required input data.frames for ftmsRanalysis package showing the first few rows and columns of each.
Table 2.
Chemical property calculations available within ftmsRanalysis.
Fig 1.
(A) Log2-transformed peak intensity profiles for each sample colored by group. (B) Number of peaks observed in each sample colored by group. (C) Histogram of all observed masses, with masses colored in blue representing those that would be retained after application of a mass_filter(). (D) Barchart corresponding to the minimum number of samples for which a peak was observed, with the height of the bar giving the number of peaks for which this is true for 1 to 20 samples. The highlighted bar gives the number of peaks remaining if the molecule_filter() requiring a peak to be observed in two or more samples is applied.
Fig 2.
(A) Kendrick plot for EM0011_sample. (B) NOSC histogram and density curve for observed peaks for the EM0011_sample.
Fig 3.
(A) Van Krevelen plot for Michigan switchgrass samples with points colored by the number of samples in which the compound was observed colored by number of observations. (B) Individual sample and group-level modified AI density curves for Michigan switchgrass.
Fig 4.
(A) Van Krevelen plot of peaks uniquely observed in Michigan corn and Michigan switchgrass samples. (B) NOSC density curves for Michigan corn and switchgrass groups.
Fig 5.
Screenshot of a Trelliscope display showing a van Krevelen plot for each sample.
The left image shows the sort/filter capability, with which characteristics of each sample (e.g. number of observed formulae) can be used to order plots. The right image shows the first page of 2x2 plots of individual samples ordered by number of observed compounds and colored by number of S atoms.