Leftover issues from QC rework
In the interest of getting the QC rework branch (https://gitlab.gwdg.de/loosolab/software/loosolab_sc_rna_framework/-/merge_requests/55) merged, I have collected the leftover issues from the branch here. Then we can work on these and merge later on:
From Fatemeh:
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It is better to have label_genes()
interactive so that user can also add annotations of their own. On the other hand, mitochondrial genes labeling might differ in different organisms. so in this way, we make sure that the labeling step counts them correctly. !338 (merged) -
a Histogram that shows the distribution of total_count and gene_per_cell over the data/conditions, would be helpful in addition to the violin plot to decide better about the lower and upper filtering thresholds.
Regarding the possibility to overwrite automatic/interactive selection of thresholds:
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We need a ranking of the potential input as per Hendriks comment here: https://gitlab.gwdg.de/loosolab/software/loosolab_sc_rna_framework/-/merge_requests/55#note_707253. This will require a way to give the thresholds in a dict-based manner, and for this to overwrite other thresholds.
Edited by Hendrik Schultheis