commit before adding ability to choose color of marker edges
added setsOfTaxaAndColors.xlsx which is significantly different from the previous version due to multiple changes to the choice of figures over the last year
added column to setsOfTaxaAndColors.xlsx for color of marker edges, adjusted genomicMDS.m to read this new column and to use it appropriately, just about to try to make the legends combine groups of entries into single legend entries
modified genomicMDS.m to group legend entries for points of the same color into individual entries (rather than having 5 blue points as in the rows of the excel file, for example), this made me change the plotting implementation slightly, and seems to have sped up the plotting by a LARGE margin
font sizes changed, and positioning changed so that title can fit on top, tick marks adjusted, legend command moved so that it appears on top of the plot
2012-07-12-dat.mat now has square CGRs instead of rectangles.
cgr_plot.m has a few lines added to make sure the CGRs produced are squares and not rectangles { particularly the line set(gcf,'Units','centimeters','Position',[2 2 15 15]) }
dataGeneratorForGenomicMDS.m now has a section repeated. This is the FOR LOOP to calculate the CGR fo each sequence in the dataset. (it seems) for some reason the first time you run the CGR subroutine, the matrix comes out as 542x542 rather than 541x541, so we run the loop once as a "dummy run", then run the loop again for all the species.
genomicMDS.m modified: outputs the coordinates of the MDS points and the structure array for the chosen dataset, and the variable INDICES, so that we can determine where certain organisms are, and what certain points correspond to. Also introduced the new color "FungiOrange"
Updated setsOfTaxaAndColors.xlsx to whatver it was at the time of submission of paper to Genome Research.