From da461df3b2716e518fe0babaf8537a718e2f645f Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Tue, 2 Jul 2024 15:09:26 -0400
Subject: [PATCH 01/13] export testing data

---
 NAMESPACE | 3 +++
 R/data.R  | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 574e441..5854287 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(CellPhoneDB)
+export(PBMC)
+export(SCENIC)
 export(add_rl_column)
 export(build_domino)
 export(circos_ligand_receptor)
diff --git a/R/data.R b/R/data.R
index 887df41..51687be 100644
--- a/R/data.R
+++ b/R/data.R
@@ -10,6 +10,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files>
 #' @usage data("SCENIC")
+#' @export
 "SCENIC"
 
 
@@ -26,6 +27,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files/pbmc3k_sce.rds>
 #' @usage data("PBMC")
+#' @export
 "PBMC"
 
 
@@ -44,4 +46,5 @@
 #' 
 #' @source <https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz>
 #' @usage data("CellPhoneDB")
+#' @export
 "CellPhoneDB"

From fa0906fd36d7c9f35ad07236517094ff9f35b03b Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Tue, 2 Jul 2024 15:37:41 -0400
Subject: [PATCH 02/13] Revert "export testing data"

This reverts commit da461df3b2716e518fe0babaf8537a718e2f645f.
---
 NAMESPACE | 3 ---
 R/data.R  | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 5854287..574e441 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(CellPhoneDB)
-export(PBMC)
-export(SCENIC)
 export(add_rl_column)
 export(build_domino)
 export(circos_ligand_receptor)
diff --git a/R/data.R b/R/data.R
index 51687be..887df41 100644
--- a/R/data.R
+++ b/R/data.R
@@ -10,7 +10,6 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files>
 #' @usage data("SCENIC")
-#' @export
 "SCENIC"
 
 
@@ -27,7 +26,6 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files/pbmc3k_sce.rds>
 #' @usage data("PBMC")
-#' @export
 "PBMC"
 
 
@@ -46,5 +44,4 @@
 #' 
 #' @source <https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz>
 #' @usage data("CellPhoneDB")
-#' @export
 "CellPhoneDB"

From 8a0f52f0381b4003c1c9f07284bab4c911f16a90 Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 08:09:27 -0400
Subject: [PATCH 03/13] internal data objects

---
 R/data.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/data.R b/R/data.R
index 887df41..4bf9274 100644
--- a/R/data.R
+++ b/R/data.R
@@ -10,6 +10,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files>
 #' @usage data("SCENIC")
+#' @internal
 "SCENIC"
 
 
@@ -26,6 +27,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files/pbmc3k_sce.rds>
 #' @usage data("PBMC")
+#' @internal
 "PBMC"
 
 
@@ -44,4 +46,5 @@
 #' 
 #' @source <https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz>
 #' @usage data("CellPhoneDB")
+#' @internal
 "CellPhoneDB"

From 750238194effe4f9a445f539a19e0fa4ed4320f7 Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 08:13:25 -0400
Subject: [PATCH 04/13] keywords internal tag

---
 R/data.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/data.R b/R/data.R
index 4bf9274..5865392 100644
--- a/R/data.R
+++ b/R/data.R
@@ -10,7 +10,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files>
 #' @usage data("SCENIC")
-#' @internal
+#' @keywords internal
 "SCENIC"
 
 
@@ -27,7 +27,7 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files/pbmc3k_sce.rds>
 #' @usage data("PBMC")
-#' @internal
+#' @keywords internal
 "PBMC"
 
 
@@ -46,5 +46,5 @@
 #' 
 #' @source <https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz>
 #' @usage data("CellPhoneDB")
-#' @internal
+#' @keywords internal
 "CellPhoneDB"

From 9109e4e5945ddfaa0aef2b5bfa6d2cd28d8075f3 Mon Sep 17 00:00:00 2001
From: jmitchell81 <jmitchell81@users.noreply.github.com>
Date: Wed, 3 Jul 2024 12:14:54 +0000
Subject: [PATCH 05/13] Update documentation

---
 man/CellPhoneDB.Rd | 2 +-
 man/PBMC.Rd        | 2 +-
 man/SCENIC.Rd      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/man/CellPhoneDB.Rd b/man/CellPhoneDB.Rd
index 8dc7607..6a6464e 100644
--- a/man/CellPhoneDB.Rd
+++ b/man/CellPhoneDB.Rd
@@ -22,4 +22,4 @@ data("CellPhoneDB")
 \description{
 A list of four subsets of CellPhoneDB data.
 }
-\keyword{datasets}
+\keyword{internal}
diff --git a/man/PBMC.Rd b/man/PBMC.Rd
index 4903938..fa1204d 100644
--- a/man/PBMC.Rd
+++ b/man/PBMC.Rd
@@ -21,4 +21,4 @@ data("PBMC")
 \description{
 A subset of the results of PBMC RNA-seq data.
 }
-\keyword{datasets}
+\keyword{internal}
diff --git a/man/SCENIC.Rd b/man/SCENIC.Rd
index 587a691..dfc8dcd 100644
--- a/man/SCENIC.Rd
+++ b/man/SCENIC.Rd
@@ -20,4 +20,4 @@ data("SCENIC")
 \description{
 A subset of SCENIC AUCs as applied to PBMC data.
 }
-\keyword{datasets}
+\keyword{internal}

From 463f5ab55c62498e822092119e8911855938fc55 Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 08:19:44 -0400
Subject: [PATCH 06/13] revert internal keywords

---
 R/data.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/R/data.R b/R/data.R
index 5865392..887df41 100644
--- a/R/data.R
+++ b/R/data.R
@@ -10,7 +10,6 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files>
 #' @usage data("SCENIC")
-#' @keywords internal
 "SCENIC"
 
 
@@ -27,7 +26,6 @@
 #'
 #' @source <https://zenodo.org/records/10951634/files/pbmc3k_sce.rds>
 #' @usage data("PBMC")
-#' @keywords internal
 "PBMC"
 
 
@@ -46,5 +44,4 @@
 #' 
 #' @source <https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz>
 #' @usage data("CellPhoneDB")
-#' @keywords internal
 "CellPhoneDB"

From e2db2abdc86ea78aea4e5e96e2eade3d5c3351cb Mon Sep 17 00:00:00 2001
From: jmitchell81 <jmitchell81@users.noreply.github.com>
Date: Wed, 3 Jul 2024 12:43:07 +0000
Subject: [PATCH 07/13] Update documentation

---
 man/CellPhoneDB.Rd | 2 +-
 man/PBMC.Rd        | 2 +-
 man/SCENIC.Rd      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/man/CellPhoneDB.Rd b/man/CellPhoneDB.Rd
index 6a6464e..8dc7607 100644
--- a/man/CellPhoneDB.Rd
+++ b/man/CellPhoneDB.Rd
@@ -22,4 +22,4 @@ data("CellPhoneDB")
 \description{
 A list of four subsets of CellPhoneDB data.
 }
-\keyword{internal}
+\keyword{datasets}
diff --git a/man/PBMC.Rd b/man/PBMC.Rd
index fa1204d..4903938 100644
--- a/man/PBMC.Rd
+++ b/man/PBMC.Rd
@@ -21,4 +21,4 @@ data("PBMC")
 \description{
 A subset of the results of PBMC RNA-seq data.
 }
-\keyword{internal}
+\keyword{datasets}
diff --git a/man/SCENIC.Rd b/man/SCENIC.Rd
index dfc8dcd..587a691 100644
--- a/man/SCENIC.Rd
+++ b/man/SCENIC.Rd
@@ -20,4 +20,4 @@ data("SCENIC")
 \description{
 A subset of SCENIC AUCs as applied to PBMC data.
 }
-\keyword{internal}
+\keyword{datasets}

From e8a3f12926dcd208df8100115fca8834bfea988e Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 08:54:06 -0400
Subject: [PATCH 08/13] pkgdown_yml topics for internal test function

---
 _pkgdown.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 423e7b9..1a1b625 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -84,6 +84,12 @@ reference:
   - count_linkage
   - mean_ligand_expression
   - rename_clusters
+- title: "internal"
+  contents:
+  - CellPhoneDB
+  - PBMC
+  - SCENIC
+  - mock_linkage_summary
 
 navbar:
   type: light

From e515e6e64fc817a2742d8c830d8a20c3f5384457 Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 10:50:44 -0400
Subject: [PATCH 09/13] dedicated data section in pkgdown references

---
 _pkgdown.yml                    | 5 +++--
 docs/reference/CellPhoneDB.html | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)
 create mode 100644 docs/reference/CellPhoneDB.html

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 1a1b625..a8629b0 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -84,12 +84,13 @@ reference:
   - count_linkage
   - mean_ligand_expression
   - rename_clusters
-- title: "internal"
+  - mock_linkage_summary
+- title: "Data"
   contents:
   - CellPhoneDB
   - PBMC
   - SCENIC
-  - mock_linkage_summary
+  
 
 navbar:
   type: light
diff --git a/docs/reference/CellPhoneDB.html b/docs/reference/CellPhoneDB.html
new file mode 100644
index 0000000..d9d76d1
--- /dev/null
+++ b/docs/reference/CellPhoneDB.html
@@ -0,0 +1 @@
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A list of four subsets of CellPhoneDB data."><title>CellPhoneDB subset — CellPhoneDB • dominoSignal</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="CellPhoneDB subset — CellPhoneDB"><meta property="og:description" content="A list of four subsets of CellPhoneDB data."><meta property="og:image" content="https://FertigLab.github.io/dominoSignal/logo.svg"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>

From e42fc5094fb47f7d681cd6ed41d88b50df926ae7 Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 11:15:47 -0400
Subject: [PATCH 10/13] spelling mistake in issues URL

---
 vignettes/dominoSignal.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/dominoSignal.Rmd b/vignettes/dominoSignal.Rmd
index 817e623..b606497 100644
--- a/vignettes/dominoSignal.Rmd
+++ b/vignettes/dominoSignal.Rmd
@@ -346,7 +346,7 @@ circos_ligand_receptor(pbmc_dom, receptor = "CD74")
 
 ## Continued Development
 
-Since dominoSignal is a package still being developed, there are new functions and features that will be implemented in future versions. In the meantime, we have put together further information on [plotting](https://fertiglab.github.io/dominoSignal/articles/plotting_vignette) and the [domino object structure](https://fertiglab.github.io/dominoSignal/articles/domino_object_vignette) if you would like to explore more of the package's functionality. Additionally, if you find any bugs, have further questions, or want to share an idea, please let us know [here](https://github.com/FertigLab/dominoSIgnal/issues).
+Since dominoSignal is a package still being developed, there are new functions and features that will be implemented in future versions. In the meantime, we have put together further information on [plotting](https://fertiglab.github.io/dominoSignal/articles/plotting_vignette) and the [domino object structure](https://fertiglab.github.io/dominoSignal/articles/domino_object_vignette) if you would like to explore more of the package's functionality. Additionally, if you find any bugs, have further questions, or want to share an idea, please let us know [here](https://github.com/FertigLab/dominoSignal/issues).
 
 <details><summary>Vignette Build Information</summary>
 Date last built and session information:

From 39bbcc3b6d3012a748933b3e07a5c5e20c710ccc Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 11:44:25 -0400
Subject: [PATCH 11/13] summarize_linkage example cluster assignment

The revision to the summarize_linkages function had caused each cell to be assigned to its own cluster. This change perserves the original intention of swapping the cell cluster assignments between the first 120 cells with the second set of 120 cells.
---
 R/differential_fxns.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/differential_fxns.R b/R/differential_fxns.R
index 0037218..cd01d5e 100644
--- a/R/differential_fxns.R
+++ b/R/differential_fxns.R
@@ -14,8 +14,11 @@ NULL
 #' @examples
 #' example(build_domino)
 #' 
-#' #create alternative clustering
-#' clusters_tiny_alt <- setNames(c(121:240, 1:120, 241:360), names(PBMC$clusters_tiny))
+#' #create alternative clustering by shuffling cluster assignments
+#' clusters_tiny_alt <- setNames(
+#'   PBMC$clusters_tiny[c(121:240, 1:120, 241:360)], 
+#'   names(PBMC$clusters_tiny)
+#' )
 #' clusters_tiny_alt <- as.factor(clusters_tiny_alt)
 #' 
 #' #build an alternative domino object

From 43d0a349e6ac01e1dc3214bd000cd55a781abc87 Mon Sep 17 00:00:00 2001
From: jmitchell81 <jmitchell81@users.noreply.github.com>
Date: Wed, 3 Jul 2024 15:46:00 +0000
Subject: [PATCH 12/13] Update documentation

---
 man/summarize_linkages.Rd | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/man/summarize_linkages.Rd b/man/summarize_linkages.Rd
index 19e07fa..3120dc5 100644
--- a/man/summarize_linkages.Rd
+++ b/man/summarize_linkages.Rd
@@ -22,8 +22,11 @@ Creates a \code{\link[=linkage_summary]{linkage_summary()}} object storing the l
 \examples{
 example(build_domino)
 
-#create alternative clustering
-clusters_tiny_alt <- setNames(c(121:240, 1:120, 241:360), names(PBMC$clusters_tiny))
+#create alternative clustering by shuffling cluster assignments
+clusters_tiny_alt <- setNames(
+  PBMC$clusters_tiny[c(121:240, 1:120, 241:360)], 
+  names(PBMC$clusters_tiny)
+)
 clusters_tiny_alt <- as.factor(clusters_tiny_alt)
 
 #build an alternative domino object

From 9473fa9e1821f78f16899ddd0be4ce491463093b Mon Sep 17 00:00:00 2001
From: Jacob Mitchell <jmitch81@jhmi.edu>
Date: Wed, 3 Jul 2024 11:50:22 -0400
Subject: [PATCH 13/13] Update summarize_linkages.Rd

---
 man/summarize_linkages.Rd | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/man/summarize_linkages.Rd b/man/summarize_linkages.Rd
index 19e07fa..3120dc5 100644
--- a/man/summarize_linkages.Rd
+++ b/man/summarize_linkages.Rd
@@ -22,8 +22,11 @@ Creates a \code{\link[=linkage_summary]{linkage_summary()}} object storing the l
 \examples{
 example(build_domino)
 
-#create alternative clustering
-clusters_tiny_alt <- setNames(c(121:240, 1:120, 241:360), names(PBMC$clusters_tiny))
+#create alternative clustering by shuffling cluster assignments
+clusters_tiny_alt <- setNames(
+  PBMC$clusters_tiny[c(121:240, 1:120, 241:360)], 
+  names(PBMC$clusters_tiny)
+)
 clusters_tiny_alt <- as.factor(clusters_tiny_alt)
 
 #build an alternative domino object