Fix: wrong filtered gene count in 01_input_qc.html

[vucinick]

Description

In the Gene filtering section of the generated 01_input_qc.html report, it reports a wrong number of removed filtered genes, both in custom and data-sensitive tab.

Current behaviour

It reports the number of genes that aren't discarded.

Expected behaviour

It should report the number of genes that are discarded and removed from the rest of the analysis.

Fix

The error is ininst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmdand inst/Rmd/single_sample/01_input_qc_children/gene_filtering_custom.Rmd. Example:

scdrake/inst/Rmd/single_sample/01_input_qc_children/gene_filtering_qc.Rmd

Lines 13 to 14 in d92f86e

	**Removing `r sum(!drake::readd(sce_qc_gene_filter, path = drake_cache_dir))` genes with UMI per cell less than
	`r cfg$MIN_UMI` and expressed in less than `r cfg$MIN_RATIO_CELLS * 100` % of all cells.**

sce_qc_gene_filter is a logical vector where TRUE is not passing the filter, and FALSE is passing the filter. However, currently it is summing all FALSE values = all the genes that are passing the filter. It is taking a reverse values of logical vector and summing it. The fix is removing the inversion of the logical vector.

[gorgitko]

Great 👍