deprecating clonalCommunity

ncborcherding · Apr 2, 2024 · b5c17ad · b5c17ad
1 parent 82c6314
commit b5c17ad
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 biocViews: Software, ImmunoOncology, SingleCell, Classification, Annotation, Sequencing
 Depends: 
 	R (>= 4.0)
@@ -26,18 +26,18 @@ Imports: stringr,
         igraph,
         stats,
 	matrixStats
-Suggests: 
+Suggests:
+	BiocStyle, 
+	dplyr,
+	ggplot2,
 	knitr, 
-	rmarkdown, 
 	markdown,
-	BiocStyle,  
-	Seurat,
-	viridis,
 	patchwork,
-	ggplot2,
-	harmony,
+	rmarkdown, 
+	Seurat,
 	spelling,
-        testthat (>= 3.0.0)
+        testthat (>= 3.0.0),
+	viridis
 VignetteBuilder: knitr
 Language: en-US
 URL: https://github.com/ncborcherding/Ibex/

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,7 +2,6 @@
 
 export(CoNGAfy)
 export(Ibex.matrix)
-export(clonalCommunity)
 export(quietBCRgenes)
 export(runIbex)
 importFrom(Matrix,sparse.model.matrix)
@@ -15,20 +14,6 @@ importFrom(SingleCellExperiment,colData)
 importFrom(SingleCellExperiment,reducedDim)
 importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,assay)
-importFrom(bluster,DbscanParam)
-importFrom(bluster,HclustParam)
-importFrom(bluster,KNNGraphParam)
-importFrom(bluster,KmeansParam)
-importFrom(bluster,NNGraphParam)
-importFrom(bluster,PamParam)
-importFrom(bluster,SNNGraphParam)
-importFrom(bluster,SomParam)
-importFrom(bluster,clusterRows)
-importFrom(igraph,E)
-importFrom(igraph,`E<-`)
-importFrom(igraph,graph_from_edgelist)
-importFrom(igraph,simplify)
-importFrom(igraph,spectrum)
 importFrom(keras,load_model_hdf5)
 importFrom(matrixStats,colWeightedMeans)
 importFrom(reticulate,array_reshape)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 0.99.6
+------------------------
+* Implementing GitHub action workflows
+* Adding testthat framework 
+* Deprecating clonalCommunity 
+
 CHANGES IN VERSION 0.99.5
 ------------------------
 * Added geometric encoding using the BLOSUM62 matrix

diff --git a/R/clonalCommunity.R b/R/clonalCommunity.R
diff --git a/man/clonalCommunity.Rd b/man/clonalCommunity.Rd
diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd
@@ -4,7 +4,7 @@ author:
 - name: Nick Borcherding
   email: [email protected]
   affiliation: Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
-date: "April 6, 2023"
+date: "April 2, 2024"
 output:
   BiocStyle::html_document:
     toc_float: true
@@ -27,6 +27,7 @@ library(BiocStyle)
 ```{r}
 suppressMessages(library(Seurat))
 suppressMessages(library(ggplot2))
+suppressMessages(library(dplyr))
 suppressMessages(library(Ibex))
 suppressMessages(library(viridis))
 suppressMessages(library(patchwork))
@@ -241,44 +242,6 @@ plot7 <- DimPlot(ibex_example, reduction = "Ibex.umap") + NoLegend()
 plot5 + plot6 + plot7
 ```
 
-## Regressing shared feature space
-
-There is a high degree of overlap in the feature space of expanded clonotypes, not only in the adaptive receptor genes that form the clonotype, but also in potentially functional genes. To identify divergent clusters in shared clonotypes using ```clonalCommunity()```, we can use the Ibex dimensions to identify clusters in order to then regress out closely associated clonotypes.
-
-```{r}
-library(harmony)
-library(bluster)
-
-#Cluster clones
-ibex_example <- clonalCommunity(ibex_example, 
-                            reduction.name = "Ibex.KF", 
-                            cluster.parameter=NNGraphParam(k=20))
-
-#Run Harmony and new UMAP for RNA
-DefaultAssay(ibex_example) <- "RNA"
-ibex_example<- RunHarmony(ibex_example, "ibex.clusters", verbose = FALSE)
-ibex_example <- RunUMAP(ibex_example, 
-                     reduction = "harmony", 
-                     dims = 1:20, 
-                     reduction.key = "RC_UMAP_", 
-                     reduction.name = "regressClone_RNA")
-
-
-plot8 <- DimPlot(ibex_example, 
-                 reduction = "rna.umap", 
-                 group.by = "CTaa") + 
-                 NoLegend() + 
-                 scale_color_viridis(option="B", discrete = TRUE)
-
-plot9 <- DimPlot(ibex_example, 
-                 reduction = "regressClone_RNA", 
-                 group.by = "CTaa") + 
-                 NoLegend() + 
-                 scale_color_viridis(option="B", discrete = TRUE)
-
-plot8 + plot9
-```
-
 # CoNGA Reduction
 
 Recent [work](https://pubmed.ncbi.nlm.nih.gov/34426704/) has proposed using representative cells for the characterization of clonotype and gene expression relationships. In order to generate these representative cells, either a mean expression across a clone or using the PCA dimensional space to identify a single cell that has the minimum euclidean distance across a clone.