Merge pull request #235 from AlexsLemonade/sjspielman/226-figure-legend-titles

Update remaining legend titles

Author: sjspielman

content/100.figure-table-legends.md

@@ -23,7 +23,7 @@ The visualization employs the UCSC Cell Browser [@doi:10.1093/bioinformatics/bta
 
 
 <!-- Figure 2 -->
-![**Overview of the `scpca-nf` workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 tag="2" width="7in"}
+![**Overview of the `scpca-nf` workflow and download file structures.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 tag="2" width="7in"}
 
 A. Overview of `scpca-nf`, the primary workflow for processing single-cell and single-nuclei RNA-seq data for the ScPCA Portal.
 Mapping is first performed with `alevin-fry` to generate a gene-by-cell count matrix, which is read into `R` and converted into a `SingleCellExperiment` (`SCE`) object.
@@ -72,7 +72,7 @@ As in panel (H), additional files `single-cell_metadata.tsv`, `_bulk_quant.tsv`,
 
 
 <!-- Figure 3 -->
-![**ScPCA Portal project download file structure and merged object workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 tag="3" width="7in"}
+![**Consensus cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 tag="3" width="7in"}
 
 A. Expanded view of the process for adding cell type annotations within `scpca-nf`, as introduced in Figure {@fig:fig2}A.
 Cell type annotation is performed on the `Processed SCE Object`.
@@ -242,7 +242,7 @@ Third, only `SCE` files are provided for multiplexed libraries; no corresponding
 <br><br>
 
 <!-- Figure S3 -->
-![**Processing other sequencing modalities with `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s3.png?sanitize=true){#fig:figS3 tag="S3" width="7in"}
+![**Processing other sequencing modalities and merging objects with `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s3.png?sanitize=true){#fig:figS3 tag="S3" width="7in"}
 
 A. Overview of the bulk RNA-Seq workflow.
 A set of FASTQ files from libraries sequenced with bulk RNA-seq are provided as input.