add MergeRows function

zhanghao-njmu · Dec 21, 2023 · b0e49c8 · b0e49c8
1 parent 7b359a2
commit b0e49c8
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Showing 16 changed files with 444 additions and 256 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,4 +10,5 @@ renv.lock
 tmaps
 src/*.so
 src/*.o
-test.R
+test.R
+test.cpp
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -118,7 +118,7 @@ Suggests:
  umap,
  UCell,
  withr
-LinkingTo: Rcpp
+LinkingTo: Rcpp,RcppArmadillo
 RoxygenNote: 7.2.3
 Config/testthat/edition: 3
 URL: https:/zhanghao-njmu/SCP
diff --git a/NAMESPACE b/NAMESPACE
@@ -70,6 +70,7 @@ export(LineagePlot)
 export(ListDB)
 export(MNN_integrate)
 export(MatrixConvert)
+export(MergeRows)
 export(PAGAPlot)
 export(PrepareDB)
 export(PrepareEnv)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,7 +1,19 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-asMatrix <- function(rp, cp, z, nrows, ncols) {
- .Call('_SCP_asMatrix', PACKAGE = 'SCP', rp, cp, z, nrows, ncols)
+MergeRowsForDense <- function(matrix, groupings) {
+ .Call('_SCP_MergeRowsForDense', PACKAGE = 'SCP', matrix, groupings)
+}
+
+MergeRowsForSparse <- function(matrix, groupings) {
+ .Call('_SCP_MergeRowsForSparse', PACKAGE = 'SCP', matrix, groupings)
+}
+
+MergeRowsC <- function(matrix, groupings) {
+ .Call('_SCP_MergeRowsC', PACKAGE = 'SCP', matrix, groupings)
+}
+
+asMatrixC <- function(rp, cp, z, nrows, ncols) {
+ .Call('_SCP_asMatrixC', PACKAGE = 'SCP', rp, cp, z, nrows, ncols)
 }
 
diff --git a/R/SCP-analysis.R b/R/SCP-analysis.R
@@ -476,6 +476,7 @@ MatrixConvert <- function(matrix, aggregate_method = "sum", geneID_from_IDtype =
  return(matrix)
 }
 
+
 #' @export
 FindCorrelatedFeatures <- function(srt, feature, method = "ejaccard", assay = NULL, slot = "data") {
  assay <- assay %||% DefaultAssay(srt)