Preprocess pipeline yaml documentation #200
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Lilly-May
commented
Feb 27, 2024
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| - <span class="parameter">n_cells_by_counts</span> `Integer`<br> | ||
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| ### Protein-specific filtering (prot) |
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Should we still list the entire structure (obs: min / max, var: min / max) here, although there are no specific parameters in the respective sections?
Lilly-May
commented
Feb 27, 2024
| - <span class="parameter">color_by</span> `String`, Default: sample_id<br> | ||
| Specify the covariate you want to use to color the dimensionality reduction plot. | ||
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| - <span class="parameter">dim_remove</span> `TODO`<br> |
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I'm not sure in what format the dim_remove parameter should be provided. As a boolean? Or an integer?
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it's an integer, it should be the component associated with tech noise (the first normally)
Lilly-May
commented
Feb 27, 2024
bio-la
reviewed
Feb 28, 2024
bio-la
requested changes
Mar 5, 2024
| @@ -328,8 +329,8 @@ Whether applying scaling or not is still a matter of debate, as stated in the [L | |||
| Parameter for CLR normalisation. | |||
| The CLR margin determines whether you normalise per cell (as you would normalise RNA data), or by feature (recommended, due to the variable nature of protein assays). | |||
| Hence, CLR margin 0 is recommended for informative qc plots in this pipeline. | |||
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bio-la
approved these changes
Mar 6, 2024
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This PR introduces a separate documentation file for all the preprocess
pipeline.ymlparameters. Additionally, I removed all the parameter explanations from thepipeline.ymlitself to make the file easier to read.Once this PR is merged, meaning we have settled on the final format of the file, I'll also adjust the prefilled file for the preprocessing tutorial to match the structure here.
There were a few things I wasn't entirely sure about, and I'll mention those in separate comments below.