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sjspielman merged 3 commits into from
Jan 13, 2026
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Update figure links #237

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741d629
update links
sjspielman Jan 12, 2026
c9029ad
tag a couple links that were at main
sjspielman Jan 12, 2026
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Merge branch 'main' into sjspielman/207-figure-links
sjspielman Jan 13, 2026
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26 changes: 13 additions & 13 deletions content/100.figure-table-legends.md
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@@ -1,7 +1,7 @@
## Figure Titles and Legends {.page_break_before}

<!-- Figure 1 -->
![**Overview of ScPCA Portal contents.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_1.png?sanitize=true){#fig:fig1 tag="1" width="7in"}
![**Overview of ScPCA Portal contents.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_1.png?sanitize=true){#fig:fig1 tag="1" width="7in"}

A. Barplots showing sample counts across four main cancer groupings in the ScPCA Portal, with each bar displaying the number of samples for each cancer type.
Each bar is colored based on the number of samples with the indicated disease timing, and total sample counts for each cancer type are shown to the right of each bar.
Expand All @@ -23,7 +23,7 @@ The visualization employs the UCSC Cell Browser [@doi:10.1093/bioinformatics/bta


<!-- Figure 2 -->
![**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"}
![**Overview of the `scpca-nf` workflow and download file structures.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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.
Expand Down Expand Up @@ -72,7 +72,7 @@ As in panel (H), additional files `single-cell_metadata.tsv`, `_bulk_quant.tsv`,


<!-- Figure 3 -->
![**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"}
![**Consensus cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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`.
Expand All @@ -95,7 +95,7 @@ For this figure specifically, the heatmap shows only the top seven consensus cel


<!-- Figure 4 -->
![**Consensus cell type annotations in Brain and CNS tumors.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_5.png?sanitize=true){#fig:fig4 tag="4" width="7in"}
![**Consensus cell type annotations in Brain and CNS tumors.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_4.png?sanitize=true){#fig:fig4 tag="4" width="7in"}

A. Dot plot showing expression of cell-type-specific marker genes across all libraries from brain and central nervous system (CNS) tumors, excluding multiplexed libraries.
Expression is shown for each broad cell type annotation, where each broad cell type annotation is a collection of similar consensus cell type annotations.
Expand All @@ -122,7 +122,7 @@ A maximum of 10 cell type marker genes are shown for each consensus cell type an
<br><br>

<!-- Figure 5 -->
![**Cell type annotation and CNV inference on neuroblastoma samples.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_5.png?sanitize=true){#fig:fig5 tag="5" width="7in"}
![**Cell type annotation and CNV inference on neuroblastoma samples.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_5.png?sanitize=true){#fig:fig5 tag="5" width="7in"}

A. UMAP highlighting cell type annotations made with the OpenScPCA Project, collapsed into broad annotation groups, for all libraries in the neuroblastoma-only ScPCA Project `SCPCP000004` (N = 42).
The UMAP was constructed from the merged `SCPCP000004` object such that all libraries contribute an equal weight, but no batch correction was performed.
Expand All @@ -143,7 +143,7 @@ The ridge plot shown is for library `SCPCL000130`.


<!-- Figure 6 -->
![**Comparison of bulk and pseudobulk modalities.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_6.png?sanitize=true){#fig:fig6 tag="6" width="7in"}
![**Comparison of bulk and pseudobulk modalities.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_6.png?sanitize=true){#fig:fig6 tag="6" width="7in"}

A. Scatter plots colored by point density of `DESeq2`-transformed and normalized bulk RNA-seq expression compared to pseudobulk expression from single-cell/nuclei RNA-seq.
Samples with RNA-seq for both bulk and single-cell/nuclei modalities, excluding multiplexed samples, from ScPCA projects comprising brain and central nervous system tumors are shown, with the number of samples considered per project shown in parentheses.
Expand Down Expand Up @@ -183,7 +183,7 @@ The reference includes marker genes for all cell types present in each organ.
<br><br>

<!-- Figure S1 -->
![**Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figS1 tag="S1" width="7in"}
![**Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figS1 tag="S1" width="7in"}

Each panel compares metrics for six ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained from processing libraries with `salmon alevin` and `alevin-fry` or `CellRanger`.
Results shown were generated with `CellRanger v6.1.2` using default parameters for single-cell libraries and use of the `--include_introns` flag to include intronic reads for single-nuclei libraries only.
Expand All @@ -208,7 +208,7 @@ Distributions reflect broad agreement between platforms in the total number of g
<br><br>

<!-- Figure S2 -->
![**Processing additional single-cell modalities in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s2.png?sanitize=true){#fig:figS2 tag="S2" width="7in"}
![**Processing additional single-cell modalities in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s2.png?sanitize=true){#fig:figS2 tag="S2" width="7in"}

A. Overview of the `scpca-nf` workflow for processing libraries with CITE-seq or antibody-derived tag (ADT) data.
The workflow mirrors that shown in Figure {@fig:fig2}A with several differences accounting for the presence of ADT data.
Expand Down Expand Up @@ -242,7 +242,7 @@ Third, only `SCE` files are provided for multiplexed libraries; no corresponding
<br><br>

<!-- Figure S3 -->
![**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"}
![**Processing other sequencing modalities and merging objects with `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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.
Expand All @@ -265,7 +265,7 @@ For this figure specifically, the merged UMAP was constructed from a merged obje
<br><br>

<!--Figure S4-->
![**Ontology-aware consensus cell type assignment provides harmonized labels for cells.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s4.png?sanitize=true){#fig:figS4 tag="S4" width="7in"}
![**Ontology-aware consensus cell type assignment provides harmonized labels for cells.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s4.png?sanitize=true){#fig:figS4 tag="S4" width="7in"}

A. UMAP highlighting cells annotated as types of T cells with `SingleR`, `CellAssign`, `SCimilarity` as well as the associated consensus cell types for the library `SCPCL000049`.
All other cells are shown in gray.
Expand All @@ -280,7 +280,7 @@ The total per-cell CNV values were calculated by summing the total number of chr


<!-- Figure S5 -->
![**Consensus cell type annotation gene expression in other diagnosis groups.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s6.png?sanitize=true){#fig:figS5 tag="S5" width="9in"}
![**Consensus cell type annotation gene expression in other diagnosis groups.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s5.png?sanitize=true){#fig:figS5 tag="S5" width="9in"}

Dot plots showing expression of cell-type-specific marker genes across all libraries from Leukemia (A), Sarcoma (B), and Other solid tumors (C) diagnosis groups.
Expression is shown for each broad cell type annotation, where each broad cell type annotation is a collection of similar consensus cell type annotations.
Expand All @@ -290,15 +290,15 @@ Dots are colored by mean gene expression across libraries and sized proportional
<br><br>

<!-- Figure S6 -->
![***Consensus cell type annotation distributions in other diagnosis groups.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s7.png?sanitize=true){#fig:figS6 tag="S6" width="7in"}
![***Consensus cell type annotation distributions in other diagnosis groups.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s6.png?sanitize=true){#fig:figS6 tag="S6" width="7in"}

Barplots of the percentage of cells annotated as each broad consensus cell type annotation across all libraries from Leukemia (A), Sarcoma (B), and Other solid tumors (C) diagnosis groups.
Within each panel, libraries are shown grouped by diagnosis.
Each column represents the distribution of cell types within a single library.
<br><br>

<!-- Figure S7 -->
![**Comparison of bulk and pseudobulk modalities for additional projects.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s8.png?sanitize=true){#fig:figS7 tag="S7" width="7in"}
![**Comparison of bulk and pseudobulk modalities for additional projects.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s7.png?sanitize=true){#fig:figS7 tag="S7" width="7in"}

A. Scatter plots colored by point density of `DESeq2`-transformed and normalized bulk RNA-seq expression compared to pseudobulk expression from single-nuclei RNA-seq.
Projects with RNA-seq for both bulk and single-cell/nuclei modalities that are not displayed in Figure {@fig:fig6}A are shown.
Expand Down
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