add fig2 legend

content/100.figure-table-legends.md

@@ -12,3 +12,21 @@ C. Example of a project card as displayed on the "Browse" page of the ScPCA Port
 This project card is associated with project `SCPCP000009`.
 Project cards include information about the number of samples, technologies and modalities, additional sample metadata information, submitter-provided diagnoses, as well as submitter-provided abstract.
 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.**
+
+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.
+This matrix is read into R and converted into a `SingleCellExperiment` (`SCE`) object.
+This `SCE` object is exported as the `Unfiltered SCE Object` without any additional processing.
+First, empty droplets are filtered out, and the resulting `SCE` is exported as the `Filtered SCE Object`.
+Next, the filtered object undergoes additional post-processing, including filtering out low-quality cells, normalizing counts, and performing dimension reduction (principle components and UMAP embeddings).
+Finally, the object undergoes cell type annotation and is exported as the `Processed SCE Object`.
+A summary QC report as well as a supplemental cell type report are prepared and exported.
+All `SCE` files are converted to `AnnData` format and exported.
+B. Representative figures that appear in the summary QC report.
+Top row from left to right: 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`; 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; `miQC` model diagnostic plot showing the percent of mitochondrial reads in each cell against the number of genes detected in the `Filtered SCE Object`, where points are colored by the probability that the cell is compromised as determined by `miQC`.
+The `miQC` model diagnostic plot is only present for libraries that were filtered with `miQC`.
+Bottom row from left to right: The percent of mitochondrial reads in each cell, as determined either by `miQC` or by a minimum unique gene count cutoff, against the number of genes detected in each cell, where points are colored by whether the cell was kept or removed prior to normalization and dimensionality reduction; UMAP embeddings where each cell is colored by the number of genes detected; UMAP embeddings for the top four most variable genes where each cell is colored by the log-normalized gene expression.
+In the actual summary QC report, the top 12 most highly variable genes are shown.