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Add page breaks and resize images that are across multiple pages
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jaclyn-taroni committed Apr 18, 2024
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Expand Up @@ -18,6 +18,8 @@ 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.
<br><br>

{.page_break_before}

<!-- Figure 2 -->
![**Overview of the `scpca-nf` workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 tag="2" width="7in"}

Expand Down Expand Up @@ -49,6 +51,8 @@ G. UMAP embeddings of log-normalized RNA expression values for the top four most
In the actual summary QC report, the top 12 most highly variable genes are shown.
<br><br>

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<!-- Figure 3 -->
![**ScPCA Portal project download file structure and merged object workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 tag="3" width="7in"}

Expand All @@ -75,6 +79,8 @@ The UMAP is constructed from the merged object such that all libraries contribut
The libraries pictured are a subset of libraries in the ScPCA project `SCPCP000003`.
<br><br>

{.page_break_before}

<!-- Figure 4 -->
![**Cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_4.png?sanitize=true){#fig:fig4 tag="4" width="7in"}

Expand Down Expand Up @@ -196,7 +202,7 @@ Red diamonds represent the median delta median score for all cells with high-qua
<br><br>

<!--Figure S5-->
![**Cell type annotation with `CellAssign`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_s5.png?sanitize=true){#fig:figS5 tag="S5" width="7in"}
![**Cell type annotation with `CellAssign`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_s5.png?sanitize=true){#fig:figS5 tag="S5" height="8in"}

Both plots in this figure are examples of plots that display results from annotating cells with `CellAssign` that can be found in the cell type summary report, shown here for library `SCPCL000490`[@doi:10.1016/j.devcel.2022.04.003].

Expand All @@ -209,7 +215,7 @@ A value of 1 means that there is complete overlap between which cells are annota
<br><br>

<!-- Figure S6 -->
![**Assessment of cell type annotation quality.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_s6.png?sanitize=true){#fig:figS6 tag="S6" width="7in"}
![**Assessment of cell type annotation quality.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.0/figures/compiled_figures/pngs/figure_s6.png?sanitize=true){#fig:figS6 tag="S6" height="8in"}

Both plots in this figure are examples of diagnostic plots in the cell type summary report, shown for library `SCPCL000001` [@doi:10.1093/neuonc/noad207].

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