updating links for reference file and fixing versioning

FertigLab · Jun 25, 2024 · 840d468 · 840d468
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diff --git a/R/import_fxns.R b/R/import_fxns.R
@@ -666,7 +666,8 @@ add_rl_column <- function(map, map_ref, conv, new_name) {
 #'
 #' Creates a data frame of mean ligand expression for use in plotting a circos
 #' plot of ligand expression and saving tables of mean expression.
-#'
+#'us
+
 #' @param x Gene by cell expression matrix
 #' @param ligands Character vector of ligand genes to be quantified
 #' @param cell_ident Vector of cell type (identity) names for which to calculate mean ligand gene expression

diff --git a/README.md b/README.md
@@ -6,9 +6,7 @@ dominoSignal is an updated version of the original [domino](https://github.com/E
 
 ### Installation
 
-dominoSignal is undergoing active development where aspects of how data is used, analyzed, and interpreted is subject to change as new features and fixes are implemented. **v0.99.1** of dominoSignal serves as the first stable development version during these active updates for reproducible usage.
-
-dominoSignal is the continuation of Domino software hosted on the [Elisseeff-Lab GitHub](https://github.com/Elisseeff-Lab/domino). The most up to date stable version is on the [FertigLab GitHub](https://github.com/FertigLab). This version of dominoSignal can be installed using the remotes package.
+dominoSignal is the continuation of Domino software hosted on the [Elisseeff-Lab GitHub](https://github.com/Elisseeff-Lab/domino). dominoSignal is undergoing active development where aspects of how data is used, analyzed, and interpreted is subject to change as new features and fixes are implemented. The most up to date stable version is on the [FertigLab GitHub](https://github.com/FertigLab). This version of dominoSignal can be installed using the remotes package.
 
 ```r
 if(!require(remotes)){
@@ -35,7 +33,8 @@ If you use our package in your analysis, please cite us:
 
 > Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, Garmire LX, Elisseeff JH. Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics. Nat Biomed Eng. 2021 Oct;5(10):1228-1238. doi: 10.1038/s41551-021-00770-5. Epub 2021 Aug 2. PMID: 34341534; PMCID: PMC9894531.
 
-> Cherry C, Mitchell J, Nagaraj S, Krishnan K, Lvovs D, Fertig E, Elisseeff J (2024). dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing. R package version 0.99.1.
+> Cherry C, Mitchell J, Nagaraj S, Krishnan K, Lvovs D, Fertig E, Elisseeff J (2024). dominoSignal: Cell Communication Analysis for Single Cell RNA Sequencing. R package version 0.99.2.
 
 ### Contact Us
 If you find any bugs or have questions, please let us know [here](https://github.com/FertigLab/dominoSignal/issues).
+tat
diff --git a/docs/articles/domino_object_vignette.html b/docs/articles/domino_object_vignette.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   dominoSignal: dominoSignal.html
   domino_object_vignette: domino_object_vignette.html
   plotting_vignette: plotting_vignette.html
-last_built: 2024-06-25T17:33Z
+last_built: 2024-06-25T18:20Z
 urls:
   reference: https://FertigLab.github.io/dominoSignal/reference
   article: https://FertigLab.github.io/dominoSignal/articles

diff --git a/docs/reference/print-domino-method.html b/docs/reference/print-domino-method.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/inst/CITATION b/inst/CITATION
@@ -30,5 +30,5 @@ bibentry(
     person("Jennifer", "Elisseeff", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-5066-1996"))
     ),
   year     = 2024,
-  note     = "R package version 0.99.1"
+  note     = "R package version 0.99.2"
 )
diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   dominoSignal: dominoSignal.html
   domino_object_vignette: domino_object_vignette.html
   plotting_vignette: plotting_vignette.html
-last_built: 2024-06-25T17:33Z
+last_built: 2024-06-25T18:20Z
 urls:
   reference: https://FertigLab.github.io/dominoSignal/reference
   article: https://FertigLab.github.io/dominoSignal/articles

diff --git a/vignettes/domino_object_vignette.Rmd b/vignettes/domino_object_vignette.Rmd
@@ -40,32 +40,58 @@ dom <- readRDS(tmp_path)
 
 ## Object contents
 
-There is a great deal of information stored with the [domino object class]([domino-class()]):
+There is a great deal of information stored with the [domino object class](https://fertiglab.github.io/dominoSignal/reference/domino-class.html). The domino object is an S4 class object that contains a variety of information about the data set used to build the object, the calculated values, and the linkages between receptors, ligands, and transcription factors. The object is structured as follows (with some examples of the information stored within each slot:
+
 - Input Data
+
   - Information about the database used to construct the rl\_map
+
   - Inputted counts matrix
+
   - Inputted z-scored counts matrix
+
   - Inputted cluster labels
+
   - Inputted transcription factor activation scores
+
 - Calculated values
+
   - Differential expression p-values of transcription factors in each cluster
+
   - Correlation values between ligands and receptors
+
   - Median correlation between components of receptor complexes
+
 - Linkages
+
   - Complexes show the component genes of any complexes in the rl map
+
   - Receptor - ligand linkages as determined from the rl map
+
   - Transcription factor - target linkages as determined from the SCENIC analysis (or other regulon inference method)
+
   - Transcription factors that are differentially expressed in each cluster
+
   - Transcription factors that are correlated with receptors
+
   - Transcription factors that are correlated with receptors in each cluster
+
   - Receptors which are active in each cluster
+
   - Ligands that may activate a receptor in a given cluster (so-called incoming ligands; these may include ligands from outside the data set)
+
 - Signaling matrices
+
   - For each cluster, incoming ligands and the clusters within the data set that they are coming from
+
   - A summary of signaling between all clusters
+
 - Miscellaneous Information
+
   - Build information, which includes the parameters used to build the object in the `build_domino()` functions
+
   - The pared down receptor ligand map information used in building the object
+
   - The percent expression of receptors within each cluster
 
 For commonly accessed information (the number of cells, clusters, and some build information), the show and print methods for domino objects can be used.