Bug exclude genes

[ktrns]

• Fixes issue #88
• Fixes custom log normalisation to allow exclusion of highly expressed genes
• Generalises assay of raw data into variable so we can later apply the workflow to spatial data #87
• Uses " for quotation marks
• Uses BE (analyse (i.e. "yse"), normalize (i.e. "ize"), colour (i.e. "our")

[ktrns]

Sorry, no PR without changes :-)

Regarding the assay_raw: You also need to change the function ExportToCerebro a bit since there it is still hard-coded "RNA":

  cerebroApp::exportFromSeurat(sc,
                               assay=assay,
                               slot="data",
                               file=path,
                               experiment_name="na",
                               organism="na",
                               groups=c("orig.ident", "seurat_clusters"),
                               cell_cycle=c("Phase"),
                               nUMI="nCount_RNA",
                               nGene="nFeature_RNA",
                               add_all_meta_data=TRUE,
                               use_delayed_array=delayed_array,
                               verbose=FALSE)

Maybe just pass nUMI and nGene as additional arguments...

Du Fuchs :-), I did set the cerebro chunk to eval=FALSE for my spatial data, but you found out that I haven't cared about the Cerebro export! Well done. I changed it, should work now.

Thanks for the review! I adapted the changes, and will re-run the script now and push the changes. Let's briefly discuss this one question above before merging.

Best & thanks a lot Katrin