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prabhakarlab · Apr 16, 2022 · 8124f77 · 8124f77
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diff --git a/R/data.R b/R/data.R
@@ -8,7 +8,7 @@
 #' @format A list with 2 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
-#' \item{locations}{data.frame} cell centroids in 2D)
+#' \item{locations}{(data.frame) cell centroids in 2D}
 #' }
 #' 
 #' @usage data(hippocampus)
@@ -68,7 +68,7 @@
 #' In addition, the spatial genes used for HMRF analysis in the
 #' reference are included.
 #'
-#' @format A list with 3 entries:
+#' @format A list with 4 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
 #' \item{locations}{(data.frame) cell centroids in 2D}
@@ -91,7 +91,7 @@
 #' count normalized and subset to 7,319 genes obtained by taking the union of
 #' the top 3,000 genes in each sample for subject 3.
 #'
-#' @format A list with 3 entries:
+#' @format A list with 2 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
 #' \item{locations}{(data.frame) spot locations in 2D}
@@ -112,7 +112,7 @@
 #' count normalized and subset to 7,319 genes obtained by taking the union of
 #' the top 3,000 genes in each sample for subject 3.
 #'
-#' @format A list with 3 entries:
+#' @format A list with 2 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
 #' \item{locations}{(data.frame) spot locations in 2D}
@@ -133,7 +133,7 @@
 #' count normalized and subset to 7,319 genes obtained by taking the union of
 #' the top 3,000 genes in each sample for subject 3.
 #'
-#' @format A list with 3 entries:
+#' @format A list with 2 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
 #' \item{locations}{(data.frame) spot locations in 2D}
@@ -154,7 +154,7 @@
 #' count normalized and subset to 7,319 genes obtained by taking the union of
 #' the top 3,000 genes in each sample for subject 3.
 #'
-#' @format A list with 3 entries:
+#' @format A list with 2 entries:
 #' \describe{
 #' \item{expression}{(matrix) gene expression matrix}
 #' \item{locations}{(data.frame) spot locations in 2D}

diff --git a/README.Rmd b/README.Rmd
@@ -58,7 +58,7 @@ usage, along with several vignettes which detail different use cases:
   Introduction to the *BanksyObject* class which serves as a container for 
   *Banksy*.  
 
-* [Mouse hippocampus MERFISH dataset](https://prabhakarlab.github.io/Banksy/articles/hippocampus-analysis.html):
+* [Mouse hippocampus VeraFISH dataset](https://prabhakarlab.github.io/Banksy/articles/hippocampus-analysis.html):
   Illustrates a grid search of parameters which best cluster cells.  
 
 * [Human dorsolateral prefrontal cortex 10x Visium dataset](https://prabhakarlab.github.io/Banksy/articles/dlpfc-analysis.html):

diff --git a/README.md b/README.md
@@ -51,7 +51,7 @@ detail different use cases:
     Introduction to the *BanksyObject* class which serves as a container
     for *Banksy*.
 
--   [Mouse hippocampus MERFISH
+-   [Mouse hippocampus VeraFISH
     dataset](https://prabhakarlab.github.io/Banksy/articles/hippocampus-analysis.html):
     Illustrates a grid search of parameters which best cluster cells.
 

diff --git a/docs/articles/banksy-object.html b/docs/articles/banksy-object.html
diff --git a/docs/articles/banksy-object_files/figure-html/subset2-1.png b/docs/articles/banksy-object_files/figure-html/subset2-1.png
diff --git a/docs/articles/banksy-object_files/figure-html/subset3-1.png b/docs/articles/banksy-object_files/figure-html/subset3-1.png
diff --git a/docs/articles/hippocampus-analysis.html b/docs/articles/hippocampus-analysis.html
diff --git a/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png b/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png
diff --git a/docs/articles/hippocampus-analysis_files/figure-html/out-1.png b/docs/articles/hippocampus-analysis_files/figure-html/out-1.png
diff --git a/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png b/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png
diff --git a/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png b/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png
diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png b/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png
diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png b/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png
diff --git a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png
diff --git a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   hippocampus-analysis: hippocampus-analysis.html
   hypothalamus-analysis: hypothalamus-analysis.html
   single-cell-exp: single-cell-exp.html
-last_built: 2022-04-16T18:04Z
+last_built: 2022-04-16T19:26Z
 urls:
   reference: https://prabhakarlab.github.io/Banksy/reference
   article: https://prabhakarlab.github.io/Banksy/articles

diff --git a/docs/reference/dlpfc151673.html b/docs/reference/dlpfc151673.html
diff --git a/docs/reference/dlpfc151674.html b/docs/reference/dlpfc151674.html
diff --git a/docs/reference/dlpfc151675.html b/docs/reference/dlpfc151675.html
diff --git a/docs/reference/dlpfc151676.html b/docs/reference/dlpfc151676.html
diff --git a/docs/reference/getARI.html b/docs/reference/getARI.html
diff --git a/docs/reference/hippocampus.html b/docs/reference/hippocampus.html
diff --git a/docs/reference/plotARI-1.png b/docs/reference/plotARI-1.png
diff --git a/docs/reference/plotAlluvia-1.png b/docs/reference/plotAlluvia-1.png
diff --git a/docs/reference/plotHeatmap-1.png b/docs/reference/plotHeatmap-1.png
diff --git a/docs/reference/plotReduction-1.png b/docs/reference/plotReduction-1.png
diff --git a/docs/reference/plotScree-1.png b/docs/reference/plotScree-1.png
diff --git a/docs/reference/plotSpatial-1.png b/docs/reference/plotSpatial-1.png
diff --git a/docs/reference/plotSpatialFeatures-1.png b/docs/reference/plotSpatialFeatures-1.png
diff --git a/docs/reference/visualcortex.html b/docs/reference/visualcortex.html
diff --git a/man/dlpfc151673.Rd b/man/dlpfc151673.Rd
diff --git a/man/dlpfc151674.Rd b/man/dlpfc151674.Rd
diff --git a/man/dlpfc151675.Rd b/man/dlpfc151675.Rd
diff --git a/man/dlpfc151676.Rd b/man/dlpfc151676.Rd
diff --git a/man/hippocampus.Rd b/man/hippocampus.Rd
diff --git a/man/visualcortex.Rd b/man/visualcortex.Rd