From 8a418eb7d69d9cd5bb96154b820e3a19f20a7084 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 11 Mar 2024 10:11:17 -0500 Subject: [PATCH 1/4] add legend for table s2 --- content/100.figure-table-legends.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 4bed885..5d28fd9 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -186,6 +186,19 @@ The workflow directly returns the results from running `spaceranger` without any

+ +**Table S2. Summary of references used for CellAssign.** +This table provides a summary of the references used for assigning cell types for fScPCA projects using `CellAssign`. +All references were built by selecting all cell types from a specified set of organs present in the marker gene list from `PanglaoDB`. + +`scpca_project_id`: ScPCA project unique identifier. +`Diagnoses`: Full set of diagnoses for all samples associated with the project. +`ScPCA reference name`: Name used to describe the custom reference. +`PanglaoDB organs included in reference`: A list of all organs that were selected to be included in the reference. +Marker genes for all cell types for each organ listed were included when constructing the reference. + +

+ ![**Assessment of cell type annotation quality.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s4.png?sanitize=true){#fig:figs4 tag="S4" width="7in"} From 382f5a8bd64de40fd941d784ddc9001038d43993 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 11 Mar 2024 10:26:22 -0500 Subject: [PATCH 2/4] remove extra f --- 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 5d28fd9..ebeed5f 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -188,7 +188,7 @@ The workflow directly returns the results from running `spaceranger` without any **Table S2. Summary of references used for CellAssign.** -This table provides a summary of the references used for assigning cell types for fScPCA projects using `CellAssign`. +This table provides a summary of the references used for assigning cell types for ScPCA projects using `CellAssign`. All references were built by selecting all cell types from a specified set of organs present in the marker gene list from `PanglaoDB`. `scpca_project_id`: ScPCA project unique identifier. From 50d06507f09dc81e61bc3581a045fa6a8fbd9fd0 Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 11 Mar 2024 11:15:57 -0500 Subject: [PATCH 3/4] Apply suggestions from code review Co-authored-by: Stephanie Spielman --- 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 ebeed5f..98540cb 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -187,9 +187,9 @@ The workflow directly returns the results from running `spaceranger` without any

-**Table S2. Summary of references used for CellAssign.** +**Table S2. Summary of references used for cell type annotation with `CellAssign`.** This table provides a summary of the references used for assigning cell types for ScPCA projects using `CellAssign`. -All references were built by selecting all cell types from a specified set of organs present in the marker gene list from `PanglaoDB`. +All references were built using all cell types from a specified set of organs present in `PanglaoDB`'s marker gene list. `scpca_project_id`: ScPCA project unique identifier. `Diagnoses`: Full set of diagnoses for all samples associated with the project. From e8909fb19af6fd296903a2e8c7137b851e0fcaea Mon Sep 17 00:00:00 2001 From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> Date: Mon, 11 Mar 2024 11:20:12 -0500 Subject: [PATCH 4/4] move legend and add some clarifying language --- content/100.figure-table-legends.md | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 98540cb..161b884 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -111,8 +111,21 @@ 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. +

+ +**Table S2. Summary of references used for cell type annotation with `CellAssign`.** +This table provides a summary of the references used for assigning cell types for ScPCA projects using `CellAssign`. +All references were built using all cell types from a specified set of organs present in `PanglaoDB`'s marker gene list. + +`scpca_project_id`: ScPCA project unique identifier. +`Diagnoses`: Full set of diagnoses for all samples associated with the project. +`ScPCA reference name`: Name used to describe the custom reference. +`PanglaoDB organs included in reference`: A list of all organs included in the reference with names of organs corresponding to organs listed in `PanglaoDB`. +The reference includes marker genes for all cell types present in each organ. +

+ ![**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"} @@ -186,18 +199,7 @@ The workflow directly returns the results from running `spaceranger` without any

- -**Table S2. Summary of references used for cell type annotation with `CellAssign`.** -This table provides a summary of the references used for assigning cell types for ScPCA projects using `CellAssign`. -All references were built using all cell types from a specified set of organs present in `PanglaoDB`'s marker gene list. - -`scpca_project_id`: ScPCA project unique identifier. -`Diagnoses`: Full set of diagnoses for all samples associated with the project. -`ScPCA reference name`: Name used to describe the custom reference. -`PanglaoDB organs included in reference`: A list of all organs that were selected to be included in the reference. -Marker genes for all cell types for each organ listed were included when constructing the reference. -

![**Assessment of cell type annotation quality.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s4.png?sanitize=true){#fig:figs4 tag="S4" width="7in"}