Closed Oliver-D-B closed 3 years ago
ktrns
commented
4 years ago Hi there,
That is totally possible and a good idea. We should add colour assignments to the meta data. I will talk to @andpet0101 about it, he handled the meta data so far. I would think that we just add another two columns for colour_sample and colour_cluster.
Our plan is to soon-ish change a few more things on the main script, so I can directly incorporate this change.
Best Katrin
andpet0101
commented
3 years ago Hi,
I think we can included named colour lists for sample and cluster in the misc slot of the Seurat object. One can even think about a named list for colours where the names correspond to metadata column names (seurat_cluster for cluster, orig.ident for sample) and the values are colour lists specifing the colour for each unique value of that column.
Best,
Andreas
There is no direct synchronization of color assignments between what is used in the scrnaseq-analysis report and what is shown in this app (e.g. colors specifically assigned to individual clusters for a given project). Actually, color assignments differ between report and app and this is confusing for users. Is there any way to transmit all relevant coloring information from a given report (or better from the report’s output folder) to be available for upload into the app (e.g. along with the .rds file)? Maybe @ktrns can help to provide an additional output from the main scrnaseq-analysis script (as input for the app)?