ref for fig2

content/100.figure-table-legends.md

@@ -14,8 +14,7 @@ Project cards include information about the number of samples, technologies and
 Where available, submitter-provided citation information as well as other databases where this data has been deposited are also provided.
 
 
-**Figure 2. Overview of ScPCA Portal workflow.**
-
+![**Figure 2. Overview of ScPCA Portal workflow.**](https://github.com/AlexsLemonade/scpca-paper-figures/blob/main/figures/compiled_figures/pngs/figure_2.png){#fig:fig2 width="7in"}
 A. Primary workflow for processing single-cell and single-nuclei 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.
 This `SCE` object is exported as the `Unfiltered SCE Object` before further post-processing.
@@ -24,7 +23,6 @@ The filtered object undergoes additional post-processing, including filtering ou
 The object undergoes cell type annotation and is exported as the `Processed SCE Object`.
 A summary QC report and a supplemental cell type report are prepared and exported.
 Finally, all `SCE` files are converted to `AnnData` format and exported.
-
 Panels B-G show example figures that appear in the summary QC report, shown here for `SCPCL000001`, as follows.
 B. The total UMI count for each droplet against the droplet's rank, where points are colored by the percentage of droplets that pass the cell filter used to create the `Filtered SCE Object`.
 C. The number of genes detected for each cell passing the cell filter again the total UMI count, where points are colored by the percentage of mitochondrial reads in the cell.