From 8fca81baa62d54274ae0ecee7f8d23afb9894070 Mon Sep 17 00:00:00 2001
From: reyvnth <revanth.krishna@cuanschutz.edu>
Date: Fri, 31 May 2024 15:33:41 -0600
Subject: [PATCH] loe package deletion and make.KNNG update

---
 DESCRIPTION                     |  3 +--
 NAMESPACE                       |  1 -
 R/expression_adjacency_matrix.R |  3 +--
 R/makeKNNG.R                    | 23 +++++++++++++++++++++++
 citation.cff                    | 18 ++++++++++++++++++
 5 files changed, 43 insertions(+), 5 deletions(-)
 create mode 100644 R/makeKNNG.R
 create mode 100644 citation.cff

diff --git a/DESCRIPTION b/DESCRIPTION
index 7523866..adfd57b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,7 @@ Date: 2024-01-24
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://github.com/fanzhanglab/STew
 BugReports: https://github.com/fanzhanglab/STew/issues
 Depends: 
@@ -23,7 +23,6 @@ Remotes:
     JEFworks-Lab/MERINGUE,
     satijalab/Seurat
 Imports:
-    loe (>= 1.1),
     Matrix (>= 1.5.4),
     ggpubr (>= 0.6.0),
     future,
diff --git a/NAMESPACE b/NAMESPACE
index 06ab64c..5c9966d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -31,7 +31,6 @@ import(ggplot2)
 import(ggpubr)
 import(ggrepel)
 import(gridExtra)
-import(loe)
 import(matrixStats)
 import(parallel)
 import(parameters)
diff --git a/R/expression_adjacency_matrix.R b/R/expression_adjacency_matrix.R
index b5bbd64..0f3cd14 100644
--- a/R/expression_adjacency_matrix.R
+++ b/R/expression_adjacency_matrix.R
@@ -9,8 +9,7 @@
 #'
 #' @export
 #'
-#'@import loe
-#'Matrix
+#'@import Matrix
 expression_adjacency_matrix <- function(obj, nk = 200, symm = FALSE, weight = TRUE, mode = "undirected", weighted = FALSE) {
   # Calculate the Euclidean distance between each pair of cells using the gene expression matrix
   mat <- t(obj$count_exp)
diff --git a/R/makeKNNG.R b/R/makeKNNG.R
new file mode 100644
index 0000000..670e991
--- /dev/null
+++ b/R/makeKNNG.R
@@ -0,0 +1,23 @@
+make.kNNG <-
+  function(DM, k=as.integer( 2*log(nrow(DM)) ), symm =FALSE, weight=FALSE ) {#begin function
+    N <- nrow(DM)
+    ADM <- matrix(0, N, N)
+    #Search kNN point
+    if(weight==TRUE){
+      for (i in 1:N) {
+        nid <- order(DM[i,])
+        ADM[ i, nid[2:(k+1)] ] <- DM[ i, nid[2:(k+1)] ]
+      }
+    }else{
+      for (i in 1:N) {
+        nid <- order(DM[i,])
+        ADM[i,nid[2:(k+1)] ] <- 1
+      }
+    }
+    if(symm==TRUE){
+      SADM <- ADM+t(ADM)
+      SADM[SADM==2*ADM] <- ADM[SADM==2*ADM]
+      ADM <- SADM
+    }
+    return(ADM)
+  }
diff --git a/citation.cff b/citation.cff
new file mode 100644
index 0000000..e85819a
--- /dev/null
+++ b/citation.cff
@@ -0,0 +1,18 @@
+cff-version: 1.0.3
+message: "If you use this software, please cite it using the following reference."
+authors:
+  - family-names: Guo
+    given-names: N.
+  - family-names: Vargas
+    given-names: J.
+  - family-names: Fritz
+    given-names: D.
+  - family-names: Krishna
+    given-names: R.
+  - family-names: Zhang
+    given-names: F.
+title: "Uncover spatially informed variations for single-cell spatial transcriptomics with STew"
+date-released: 2024
+url: "https://doi.org/10.1093/bioadv/vbae064"
+journal: "Bioinformatics Advances"
+doi: "10.1093/bioadv/vbae064"