From 0ad637c199a254639ab2ae879f1eab2516147119 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Feb 2024 14:54:29 -0500 Subject: [PATCH 1/7] table s1 legend --- content/100.figure-table-legends.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index d895c19..59dcdc7 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -84,3 +84,19 @@ B. Example heatmap as shown in the cell type summary report comparing annotation Heatmap cells are colored by the Jaccard similarity index. A value of 1 means that there is complete overlap between which cells are annotated with the two labels being compared, and a value of 0 means that there is no overlap between which cells are annotated with the two labels being compared. The heatmap shown is from library `SCPCL000498`. + + +## Supplementary Figures and Tables + +**Table S1. Overview of ScPCA Portal Datasets.** +This table provides descriptions and sample and library counts for each project in the ScPCA Portal. + +`scpca_project_id`: ScPCA project unique identifier. +`Diagnosis group`: Diagnosis group as shown in Figure {@fig:fig1}. +`Diagnoses`: Full set of diagnoses for all samples associated with the project. +`Total number of samples (S)`: Number of samples associated with the project. +`Total number of libraries (L)`: Number of libraries associated with the project. +Due to additional sequencing modalities and/or multiplexing, projects may have more libraries than samples. +All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension or additional modality. + + From a891bc43311aae86e25caf84026fb75a95fe087b Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Feb 2024 16:05:38 -0500 Subject: [PATCH 2/7] fig s1 legend, initial commit --- content/100.figure-table-legends.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 59dcdc7..72f0049 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -100,3 +100,20 @@ Due to additional sequencing modalities and/or multiplexing, projects may have m All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension or additional modality. +![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs3 width="7in"} + +Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained when processing data with both `alevin-fry` and `CellRanger`. +Panels B-D consider only cells present in both the `alevin-fry` and `CellRanger` output. + +A. Runtime in minutes (top row) and peak memory in GB (bottom row) for six ScPCA libraries processed with `alevin-fry` and `CellRanger`. +Processing with `alevin-fry` was consistently faster and more memory-efficient compared to processing with `CellRanger`. + +B. Comparison of mean gene expression values for six ScPCA libraries processed with `alevin-fry` and `CellRanger`, shown on a log-scale. +Each point is a gene, and only genes detected in at least 5 cells are shown. +$R^2$ values shown in the top left corner of each panel reflect broad agreement in mean gene expression values between platforms. + +C. Comparison of log total UMI counts for six ScPCA libraries processed with `alevin-fry` and `CellRanger`. +Distributions reflect broad agreement in the total UMI count per cell between platforms, although `alevin-fry` returned slightly higher values for certain single-cell libraries. + +D. Comparison of log total genes per cell for six ScPCA libraries processed with `alevin-fry` and `CellRanger`. +Distributions reflect broad agreement between platforms in the total number of genes per cell between platforms, although `alevin-fry` returned slightly higher values for certain single-cell libraries. From 5a692fc66f980dbd3c75f7e052d690a469e0f5d0 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Feb 2024 16:07:19 -0500 Subject: [PATCH 3/7] move that sentence maybe --- content/100.figure-table-legends.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 72f0049..f7699ef 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -103,11 +103,12 @@ All remaining columns give the number of libraries (as designated with `(L)`) wi ![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs3 width="7in"} Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained when processing data with both `alevin-fry` and `CellRanger`. -Panels B-D consider only cells present in both the `alevin-fry` and `CellRanger` output. A. Runtime in minutes (top row) and peak memory in GB (bottom row) for six ScPCA libraries processed with `alevin-fry` and `CellRanger`. Processing with `alevin-fry` was consistently faster and more memory-efficient compared to processing with `CellRanger`. +Panels B-D show only cells present in both the `alevin-fry` and `CellRanger` output. + B. Comparison of mean gene expression values for six ScPCA libraries processed with `alevin-fry` and `CellRanger`, shown on a log-scale. Each point is a gene, and only genes detected in at least 5 cells are shown. $R^2$ values shown in the top left corner of each panel reflect broad agreement in mean gene expression values between platforms. From 31afd5b8e0e838574feb962f2f06b2a056362418 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Feb 2024 16:18:09 -0500 Subject: [PATCH 4/7] figs1 is figs1, not figs3 --- content/100.figure-table-legends.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index f7699ef..29a571d 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -100,7 +100,7 @@ Due to additional sequencing modalities and/or multiplexing, projects may have m All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension or additional modality. -![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs3 width="7in"} +![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs1 width="7in"} Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained when processing data with both `alevin-fry` and `CellRanger`. From 3d387bceb19628b0fb9f76a9cbf4e7d7c40e176b Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Mon, 4 Mar 2024 11:59:40 -0500 Subject: [PATCH 5/7] Apply suggestions from code review Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- content/100.figure-table-legends.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 29a571d..0f9ca4a 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -97,12 +97,12 @@ This table provides descriptions and sample and library counts for each project `Total number of samples (S)`: Number of samples associated with the project. `Total number of libraries (L)`: Number of libraries associated with the project. Due to additional sequencing modalities and/or multiplexing, projects may have more libraries than samples. -All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension or additional modality. +All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension type or additional modality. ![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs1 width="7in"} -Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained when processing data with both `alevin-fry` and `CellRanger`. +Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained from processing libraries with both `alevin-fry` and `CellRanger`. A. Runtime in minutes (top row) and peak memory in GB (bottom row) for six ScPCA libraries processed with `alevin-fry` and `CellRanger`. Processing with `alevin-fry` was consistently faster and more memory-efficient compared to processing with `CellRanger`. From 3fd7290cc7977bc9cf451db136cb09c4535bee33 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 4 Mar 2024 12:01:35 -0500 Subject: [PATCH 6/7] dont duplicate Figure titles and hopefully fix supplmental labeling --- content/100.figure-table-legends.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 0f9ca4a..bd4bae9 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -1,6 +1,6 @@ ## Figure Titles and Legends -![**Figure 1. Overview of ScPCA Portal contents.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_1.png?sanitize=true){#fig:fig1 width="7in"} +![**Overview of ScPCA Portal contents.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_1.png?sanitize=true){#fig:fig1 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 shaded based on the number of samples with each disease timing, and total sample counts for each cancer type are shown to the right of each bar. @@ -17,7 +17,7 @@ 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 the `scpca-nf` workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 width="7in"} +![**Overview of the `scpca-nf` workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 width="7in"} A. An overview of `scpca-nf`, the 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. @@ -47,7 +47,7 @@ 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. -![**Figure 3. ScPCA Portal project download file structure and merged object workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 width="7in"} +![**ScPCA Portal project download file structure and merged object workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 width="7in"} A. File download structure for an ScPCA Portal project download in `SingleCellExperiment` (`SCE`) format. The download folder is named according to both the project ID and the date it was downloaded. @@ -72,7 +72,7 @@ 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`. -![**Figure 4. Cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_4.png?sanitize=true){#fig:fig4 width="7in"} +![**Cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_4.png?sanitize=true){#fig:fig4 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`. @@ -100,7 +100,7 @@ Due to additional sequencing modalities and/or multiplexing, projects may have m All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension type or additional modality. -![**Figure S1. Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs1 width="7in"} +![**Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs1 tag="S1" width="7in"} Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained from processing libraries with both `alevin-fry` and `CellRanger`. From e35d2a2fa4beb98802dbfc48af4d0efa5cdc6bf3 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 4 Mar 2024 12:06:29 -0500 Subject: [PATCH 7/7] add spacing so it's clearer which legend belongs with which figure, as well as guiding comments --- content/100.figure-table-legends.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index bd4bae9..ea91241 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -1,5 +1,8 @@ ## Figure Titles and Legends +

+ + ![**Overview of ScPCA Portal contents.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_1.png?sanitize=true){#fig:fig1 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. @@ -16,7 +19,9 @@ 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. +

+ ![**Overview of the `scpca-nf` workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_2.png?sanitize=true){#fig:fig2 width="7in"} A. An overview of `scpca-nf`, the primary workflow for processing single-cell and single-nuclei data for the ScPCA Portal. @@ -46,7 +51,9 @@ F. UMAP embeddings of log-normalized RNA expression values where each cell is co G. UMAP embeddings of log-normalized RNA expression values for the top four most variable genes, colored by the given gene's expression. In the actual summary QC report, the top 12 most highly variable genes are shown. +

+ ![**ScPCA Portal project download file structure and merged object workflow.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_3.png?sanitize=true){#fig:fig3 width="7in"} A. File download structure for an ScPCA Portal project download in `SingleCellExperiment` (`SCE`) format. @@ -71,7 +78,9 @@ A grid of UMAPs is shown for each library in the merged object, with cells in th The UMAP is constructed from the merged object such that all libraries contribute an equal weight, but no batch correction was performed. The libraries pictured are a subset of libraries in the ScPCA project `SCPCP000003`. +

+ ![**Cell type annotation in `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_4.png?sanitize=true){#fig:fig4 width="7in"} A. Expanded view of the process for adding cell type annotations within `scpca-nf`, as introduced in Figure {@fig:fig2}A. @@ -88,6 +97,9 @@ The heatmap shown is from library `SCPCL000498`. ## Supplementary Figures and Tables +

+ + **Table S1. Overview of ScPCA Portal Datasets.** This table provides descriptions and sample and library counts for each project in the ScPCA Portal. @@ -99,7 +111,9 @@ This table provides descriptions and sample and library counts for each project Due to additional sequencing modalities and/or multiplexing, projects may have more libraries than samples. All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension type or additional modality. +

+ ![**Results from benchmarking `alevin-fry` and `CellRanger` performance.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s1.png?sanitize=true){#fig:figs1 tag="S1" width="7in"} Each panel compares metrics for six representative ScPCA libraries, including three single-cell and three single-nuclei suspensions, obtained from processing libraries with both `alevin-fry` and `CellRanger`.