update support for LR-velo

welch-lab · Mar 9, 2023 · b56995b · b56995b
1 parent 45d5884
commit b56995b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cytosignal
 Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Version: 0.2.0
 Type: Package
 Authors@R: 
     person(given = "Jialin",

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,10 +10,13 @@ S3method(graphNicheLR,CytoSignal)
 S3method(graphNicheLR,dgCMatrix)
 S3method(imputeNiche,CytoSignal)
 S3method(imputeNiche,dgCMatrix)
+S3method(imputeNicheVelo,CytoSignal)
 S3method(inferScoreLR,CytoSignal)
 S3method(inferScoreLR,dgCMatrix)
 S3method(inferSignif,CytoSignal)
 S3method(inferSignif,matrix_like)
+S3method(inferVeloLR,CytoSignal)
+S3method(inferVeloLR,matrix_like)
 S3method(normCounts,CytoSignal)
 S3method(normCounts,dgCMatrix)
 S3method(normCounts,list)
@@ -31,10 +34,13 @@ export(hex_bin)
 export(hex_coord)
 export(hex_pos)
 export(imputeNiche)
+export(imputeNicheVelo)
 export(inferEpsParams)
 export(inferScoreLR)
 export(inferSignif)
+export(inferVeloLR)
 export(normCounts)
+export(permuteImpEdge)
 export(permuteImpLR)
 export(permuteListImpLR)
 export(permuteListScoreLR)
@@ -56,6 +62,9 @@ exportClasses(ImpData)
 exportClasses(lrScores)
 exportClasses(lrVelo)
 exportMethods(show)
+importFrom(Matrix,colSums)
+importFrom(Matrix,rowSums)
+importFrom(Matrix,t)
 importFrom(RTriangle,pslg)
 importFrom(RTriangle,triangulate)
 importFrom(Rcpp,evalCpp)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -57,6 +57,10 @@ graphMeanLR_cpp <- function(alpha_list, dge_lig, lig_index, lig_list, nb_index,
     .Call('_cytosignal_graphMeanLR_cpp', PACKAGE = 'cytosignal', alpha_list, dge_lig, lig_index, lig_list, nb_index, nb_list)
 }
 
+inferVeloLR_cpp <- function(dge_lig, dge_recep, dge_lig_velo, dge_recep_velo, lig_index, lig_list, recep_index, recep_list) {
+    .Call('_cytosignal_inferVeloLR_cpp', PACKAGE = 'cytosignal', dge_lig, dge_recep, dge_lig_velo, dge_recep_velo, lig_index, lig_list, recep_index, recep_list)
+}
+
 VelographNicheLR_cpp <- function(dge_lig, dge_recep, dge_velo, lig_index, lig_list, recep_index, recep_list, nb_index, nb_list) {
     .Call('_cytosignal_VelographNicheLR_cpp', PACKAGE = 'cytosignal', dge_lig, dge_recep, dge_velo, lig_index, lig_list, recep_index, recep_list, nb_index, nb_list)
 }