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Dear all, I am a R beginner, and I am looking for a way to do the same thing for all levels of a column in a table. Basically, I have a bunch of protein sequences composed of different amino acid residues, and each residue is represented by an uppercase letter. I want to calculate the ratio of different amino acid residues at each position of the proteins. Here is an example table: Proteins

Hi list, I am using the capscale function in vegan_2.0-7 to do a constrained principal coordinates analysis, and I kept getting the following error message: Error in Y.r[, oo, drop = FALSE] : subscript out of bounds I googled but I couldn't find an answer. Could anyone tell me why this error msg and what to do? Here is the command I used:

Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of the positions, what residues are there, and the ratios of residues. The ratios of residues at a position add up to 100, or close to 100 (more on