bobermayer
commented
9 months ago looks like the default is taken as first entry in the covariate file, so we should make sure we put "replicate" last
and if "color_by" is different from X covariate it introduces position_dodge for the box plot but not for the jitter (use jitterdodge?)
The plots of the 'Gene Info' section in the GeneBrowser tab are give a useful overview of individual genes and are also the only point in seaPiper where users can take a look at expression values. However, there are some possible points of improvement:
1) The plot - while interactive - does not display any information on hovering on a given data point, which makes it quite hard to identify specific samples (i.e. outliers). Ideally hovering in this plot should display at least the Sample_Name, or the full information that is also shown on hover in the PCA plot.
2) the default choice of 'replicate' for the X-covariate can be a poor one, since this column is often also automatically by sea-snap if not manually defined and is then not properly defined (i.e. the same for all samples). In such cases users may not grasp that they have to change the plot settings to see useful information here at all.
3) The 'Symbol by' selection seems to be broken and does not change the plot (though it does reload/recreate it)