Fig S2 legend #67
Fig S2 legend #67
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Note to selves: no merging until the base is |
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This looks pretty good, I just had a few thoughts on wording mostly around the CITE-seq part. I might tag in @jashapiro to look at the multiplexed workflow legend.
content/100.figure-table-legends.md
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| @@ -138,6 +138,37 @@ Distributions reflect broad agreement between platforms in the total number of g | |||
| <!-- Figure S2 --> | |||
| {#fig:figs2 tag="S2" width="7in"} | |||
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| A. Overview of the `scpca-nf` workflow for CITE-seq libraries with antibody-derived tag (ADT) counts. | |||
| The workflow mirrors that shown in Figure {@fig:fig2}A with several differences accounting for the presence of ADT data. | |||
| First, both an RNA and ADT FASTQ file are inputted to `alevin-fry`, along with information about ADT barcodes. | |||
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| First, both an RNA and ADT FASTQ file are inputted to `alevin-fry`, along with information about ADT barcodes. | |
| First, both an RNA and ADT FASTQ file are required as input to `alevin-fry`, along with a TSV file containing infomation about ADT barcodes. |
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A related question is we want to modify the figure itself to actually show an ADT-by-cell matrix? CC @dvenprasad, currently we show only a gene-by-cell matrix (S2A: https://github.com/AlexsLemonade/scpca-paper-figures/blob/main/figures/compiled_figures/pngs/figure_s2.png)
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Hmmm I think we could, but I don't think it's entirely necessary. I'm worried about overcrowding. Maybe let's see if others have thoughts during review and you can add a comment there.
Co-authored-by: Ally Hawkins <[email protected]>
content/100.figure-table-legends.md
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| A. Overview of the `scpca-nf` workflow for processing libraries with CITE-seq or antibody-derived tag (ADT) derived data. | ||
| The workflow mirrors that shown in Figure {@fig:fig2}A with several differences accounting for the presence of ADT data. | ||
| First, both an RNA and ADT FASTQ file are required as input to `alevin-fry`, along with a TSV file containing infomation about ADT barcodes. | ||
| The gene-by-cell and ADT-by-cell count matrices are produced and read into `R` to create a `SingleCellExperiment` (SCE) object. |
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I would add an html comment here to decide on if we should add in the ADT by cell matrix to the figure.
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Will do, and once this goes in I'm also going to open an issue in the paper figures repo and link to this caption to gather thoughts there, too.
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Click the link below to download the manuscript build as a ZIP file. |
Closes #14
Stacked on #66
This PR adds the S2 legend. It could use lots of feedback all around..!
One particular spot to look at is in panel A, where I sort wrote something that is not part of the figure -
An ADT-by-cell count matrix is additionally produced and read into R along with the gene-by-cell count matrix.- the figure itself does not contain any indication of an ADT-by-cell matrix. What do you think about it? Cut it?I'm also particularly interested to hear thoughts on panel B. I tried to relate it back to Figure 2 itself, but I can't tell if that is helpful or more confusing.