hdpriest
commented
9 years ago Allow users to designate on the input page if multiple genes are plotted to the same plot, or individual plots.
Also allow users to specify if each gene should be color-coded, or if they wish to see a grey-scale gene expression trend plot (this is helpful for looking at large sets of co-expressed genes, say, N=150, as a mass of co-expressed lines)
If you can, allow users to specify box-and-whiskers plot, or line plots.
Allow users to designate only one (via radio button) of several following normalization methods: Maximum-normalized (each gene individually scaled so that each data point is a fraction of that genes maximum expression - normalizes expression on the interval 0-1)
Mean normalized (each gene scaled such that each data point is divided by the mean expression value for the data series of that gene) (DEFAULT)
Log 2 scaled
Luminarys
Expression query - a multiple gene query, selecting the genes from the expression table (Zmays_Expression), and returning the expression values.
Ideally, this would appear as line plot (maybe a xy plot), but we'll want to have a lot of flexibility: log2 scale, or not (if possible, right on the page with the graph) moving points around on the x axis
Could be difficult: Grouping points by experimental replicates (I'll tell you which goes with which), and producing replicate-group box-plots
Very difficult: dynamically switching between replicate-grouped box-plots and non grouped data.