version 0.99.7

cran · Oct 30, 2023 · ab40a6c · ab40a6c
1 parent ace993f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: inferCSN
 Title: Inferring Cell-Specific Gene Regulatory Network
-Version: 0.99.6
-Date: 2023-10-26
+Version: 0.99.7
+Date: 2023-10-30
 Authors@R: 
     person("Meng", "Xu", email = "mengxu98@qq.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8300-1054"))
 Maintainer: Meng Xu <mengxu98@qq.com>
@@ -25,7 +25,7 @@ LazyData: true
 RoxygenNote: 7.2.3
 Language: en-US
 NeedsCompilation: yes
-Packaged: 2023-10-27 08:50:49 UTC; MSI
+Packaged: 2023-10-30 09:20:37 UTC; MSI
 Author: Meng Xu [aut, cre] (<https://orcid.org/0000-0002-8300-1054>)
 Repository: CRAN
-Date/Publication: 2023-10-27 11:40:09 UTC
+Date/Publication: 2023-10-30 10:30:02 UTC
diff --git a/MD5 b/MD5
@@ -1,16 +1,16 @@
-264f59c01e021e20821196770938a2ae *DESCRIPTION
+a391abb051df2885c3f48d2f0b540673 *DESCRIPTION
 7c52ffa536a7ee404a1970079f438922 *LICENSE
 b48ef5d987897d838df5226751680a0f *NAMESPACE
 5e08e4dbc7bfa1bf575f7672aff13441 *R/RcppExports.R
 4a8c3c169d90a573af79901ddb0ca2c9 *R/auc.calculate.R
 ed324fe13967373f0ebff75d176d8d6b *R/compute.gene.rank.R
 643ade498aab0c7b5410cb03dbb9a50d *R/data.R
 569f9ac6273c770b4acbc3eb65b362fb *R/inferCSN-package.R
-92b2747f3e12209d4ea369ba887a67e8 *R/inferCSN.R
+04ca60f893ba9a71cff624d4829c186b *R/inferCSN.R
 715a9aeffcf51cf83312d5c9d6ec328c *R/network.visualization.R
 46e2da40b98966b3a562a7e424ad152f *R/sparse.regression.R
 ef4b9e9703cb364732029f703ca9f1ce *R/utils.R
-83182b662920b2607aed49c9d7b9cba0 *README.md
+e30a750b6b3c4e66b49ba068ccb9de05 *README.md
 191a298ed75823937c77adad132f746b *data/exampleGroundTruth.rda
 975775272629b1e1438f9c89883e7728 *data/exampleMatrix.rda
 57b1f401ca4e288993d509078d88d236 *man/acc.calculate.Rd
@@ -33,22 +33,22 @@ f7a5bfcd778f7d581b09d78d3eac0bb4 *man/inferCSN.Rd
 fff4dcff1db51ae21b76613e1dfed1c5 *man/print.inferCSN.Rd
 3fcd8c319587d585129534013633c858 *man/sparse.regression.Rd
 73197635a9a5df894c4f5b4e88ca4e8c *man/sub.inferCSN.Rd
-1e6750ed9d5f86b882e6a24591733b47 *src/BetaVector.cpp
+0347ffda63bae663f9354d1e0b948d57 *src/BetaVector.cpp
 dadb1987bfb2f80d199a2e25b02a051d *src/CDL012LogisticSwaps.cpp
 64737baec03e2641f58d5681381874d6 *src/CDL012SquaredHingeSwaps.cpp
-45e55da928a9a22670c9a7380e7469b1 *src/CDL012Swaps.cpp
-b9f4edd41ee1ba186d768676b2bf79ee *src/DT2Matrix.cpp
+6a4f677eff1881a88c670cf19c77773c *src/CDL012Swaps.cpp
+2e4e9b0639d3f1afc4cf99411a293b67 *src/DT2Matrix.cpp
 d4f2e65104193ad8b04b23281a39cd8c *src/Grid.cpp
-51b6baa37f71f76d69bc5e178c98b8a7 *src/Grid1D.cpp
+2ebc2a8b814581ce38dd0a53cf275ce5 *src/Grid1D.cpp
 8748c274ffef69c8dc7f2c0f88228b22 *src/Grid2D.cpp
 09837ef4410ca3aa193eb60b7a8f681b *src/Interface.cpp
 c2fbbe606dbc01e99513a08efa77bb27 *src/Makevars
 c2fbbe606dbc01e99513a08efa77bb27 *src/Makevars.win
 41bc93afdbfbce896558b943b882d7e7 *src/Normalize.cpp
 bcd102094770a2e20628f6cb0dfc4684 *src/RcppExports.cpp
 b8da420687f2f9943625f9c8cddda799 *src/Test_Interface.cpp
-053756d599fb6942fb1959c5f54f4157 *src/include/BetaVector.h
-d10d7cbeac8dd66edb8abfe537ba2e83 *src/include/CD.h
+e447698f0493b967abd0e0aaf2eca2c2 *src/include/BetaVector.h
+e9aab72b23846ad7db4b0fa1e2597d09 *src/include/CD.h
 3006562807501591e7979d1b5af7c039 *src/include/CDL0.h
 c9262d8cc37f5ad121511ab15f1ef234 *src/include/CDL012.h
 da6865571ac3a696ef96d8d10c8b7c9a *src/include/CDL012Logistic.h
@@ -61,12 +61,12 @@ c36020aa6b5463f99a6265a18d745473 *src/include/CDL012LogisticSwaps.h
 fa0e95061a24b8e548c611d4304664d0 *src/include/Grid.h
 1e34795fcfd7f91aa821223794050e00 *src/include/Grid1D.h
 5155c4b89da70421f47b4e82a0111866 *src/include/Grid2D.h
-29346ba8476c3664856ab8f5ae9ff180 *src/include/GridParams.h
+5f89a8eaba4ab540eb63046a1e83dbe6 *src/include/GridParams.h
 3754bebf455414fb993fd10bfc967742 *src/include/Interface.h
 68b70f6c4a8c08a8d7f6bb97746d3d49 *src/include/MakeCD.h
 aea94cb863ab3243b5c681f9d905c175 *src/include/Model.h
 8650499eeb16d4bf88397c8ed3c29c92 *src/include/Normalize.h
-1dab88b0db3caf456c803e72434b8cf8 *src/include/Params.h
+cdde68a3cfff76e8a18c34209800bea5 *src/include/Params.h
 0816e979947d47e1e91c6327a62d641c *src/include/Test_Interface.h
 f3a3cce4a45a5306180127b28e5aa66c *src/include/utils.h
 82ebc8c76e0a000e5bf6e391edd49ff3 *src/utils.cpp

diff --git a/R/inferCSN.R b/R/inferCSN.R
@@ -61,7 +61,7 @@ setGeneric("inferCSN",
                     maxSuppSize = NULL,
                     verbose = FALSE,
                     cores = 1) {
-             UseMethod(generic = "inferCSN")
+             UseMethod(generic = "inferCSN", object = matrix)
            })
 
 #' @rdname inferCSN

diff --git a/README.md b/README.md
@@ -6,19 +6,21 @@
 
 <!-- badges: end -->
 
+## **Introduction**
+
 [*`inferCSN`*](https://mengxu98.github.io/inferCSN/) is an package for inferring cell-specific gene regulatory network from single-cell sequencing data.
 
 <img src="man/figures/inferCSN.svg" width="75%"/>
 
-## **Install**
+## **Installation**
 
-### [*`CRAN`*](https://github.com/cran)
+You can install the released version from [*`CRAN`*](https://github.com/cran) use:
 
 ``` r
 install.packages("inferCSN")
 ```
 
-### Using [*`pak`*](https://github.com/r-lib/pak)
+You can install the development version from [*`GitHub`*](https://github.com/mengxu98/inferCSN) use [*`pak`*](https://github.com/r-lib/pak):
 
 ``` r
 if (!require("pak", quietly = TRUE)) {
@@ -27,13 +29,13 @@ if (!require("pak", quietly = TRUE)) {
 pak::pak("mengxu98/inferCSN")
 ```
 
-### Using *`git clone`*
+You can also install the development version use *`git clone`* to automatically handle some issues related to dependencies:
 
 ``` bash
 git clone https://github.com/mengxu98/inferCSN.git
 cd inferCSN
 sh scripts/requirements.sh
-R CMD INSTALL .
+R CMD INSTALL . --library=/your/lib/path
 ```
 
 ## **Usage**

diff --git a/src/BetaVector.cpp b/src/BetaVector.cpp
@@ -7,65 +7,59 @@
 std::vector<std::size_t> nnzIndicies(const arma::vec& B){
     // Returns a vector of the Non Zero Indicies of B
     const arma::ucolvec nnzs_indicies = arma::find(B);
-    return arma::conv_to<std::vector<std::size_t>>::from(nnzs_indicies); 
+    return arma::conv_to<std::vector<std::size_t>>::from(nnzs_indicies);
 }
 
-// std::vector<std::size_t> nnzIndicies(const arma::sp_mat& B){
+// std::vector<std::size_t> nnzIndicies(const arma::sp_mat& B) {
 //     // Returns a vector of the Non Zero Indicies of B
 //     std::vector<std::size_t> S;
 //     arma::sp_mat::const_iterator it;
 //     const arma::sp_mat::const_iterator it_end = B.end();
-//     for(it = B.begin(); it != it_end; ++it)
-//     {
+//     for(it = B.begin(); it != it_end; ++it) {
 //         S.push_back(it.row());
 //     }
-//     return S; 
+//     return S;
 // }
 
 std::vector<std::size_t> nnzIndicies(const arma::vec& B, const std::size_t low){
     // Returns a vector of the Non Zero Indicies of a slice of B starting at low
     // This is for NoSelectK situations
     const arma::vec B_slice = B.subvec(low, B.n_rows-1);
     const arma::ucolvec nnzs_indicies = arma::find(B_slice);
-    return arma::conv_to<std::vector<std::size_t>>::from(nnzs_indicies); 
+    return arma::conv_to<std::vector<std::size_t>>::from(nnzs_indicies);
 }
 
 // std::vector<std::size_t> nnzIndicies(const arma::sp_mat& B, const std::size_t low){
 //     // Returns a vector of the Non Zero Indicies of B
 //     std::vector<std::size_t> S;
-//     
-//     
+//
 //     arma::sp_mat::const_iterator it;
 //     const arma::sp_mat::const_iterator it_end = B.end();
-//     
-//     
-//     for(it = B.begin(); it != it_end; ++it)
-//     {
+//
+//     for(it = B.begin(); it != it_end; ++it) {
 //         if (it.row() >= low){
 //             S.push_back(it.row());
 //         }
 //     }
-//     return S; 
+//     return S;
 // }
 
 
 std::size_t n_nonzero(const arma::vec& B){
     const arma::vec nnzs = arma::nonzeros(B);
     return nnzs.n_rows;
-
 }
 
 // std::size_t n_nonzero(const arma::sp_mat& B){
 //     return B.n_nonzero;
-//     
 // }
 
 bool has_same_support(const arma::vec& B1, const arma::vec& B2){
     if (B1.size() != B2.size()){
         return false;
     }
     std::size_t n = B1.n_rows;
-    
+
     bool same_support = true;
     for (std::size_t i = 0; i < n; i++){
         same_support = same_support && ((B1.at(i) != 0) == (B2.at(i) != 0));
@@ -74,14 +68,14 @@ bool has_same_support(const arma::vec& B1, const arma::vec& B2){
 }
 
 // bool has_same_support(const arma::sp_mat& B1, const arma::sp_mat& B2){
-//     
+//
 //     if (B1.n_nonzero != B2.n_nonzero) {
 //         return false;
 //     } else {  // same number of nnz and Supp is sorted
 //         arma::sp_mat::const_iterator i1, i2;
 //         const arma::sp_mat::const_iterator i1_end = B1.end();
-//         
-//         
+//
+//
 //         for(i1 = B1.begin(), i2 = B2.begin(); i1 != i1_end; ++i1, ++i2)
 //         {
 //             if(i1.row() != i2.row())
@@ -92,4 +86,3 @@ bool has_same_support(const arma::vec& B1, const arma::vec& B2){
 //         return true;
 //     }
 // }
-
diff --git a/src/CDL012Swaps.cpp b/src/CDL012Swaps.cpp
@@ -14,7 +14,17 @@ FitResult<T> CDL012Swaps<T>::_Fit() {
     auto result = CDL012<T>(*(this->X), this->y, this->P).Fit(); // result will be maintained till the end
     this->B = result.B;
     this->b0 = result.b0;
-    double objective = result.Objective;
+
+    // Remove the following 1 line and line-93 to emilate warning:
+        // CDL012Swaps.cpp:97:16:   required from here
+        // CDL012Swaps.cpp:17:12: warning: variable 'objective' set but not used [-Wunused-but-set-variable]
+        //     17 |     double objective = result.Objective;
+        //         |            ^~~~~~~~~
+        // CDL012Swaps.cpp: In instantiation of 'FitResult<T> CDL012Swaps<T>::_Fit() [with T = arma::SpMat<double>]':
+        // CDL012Swaps.cpp:98:16:   required from here
+        // CDL012Swaps.cpp:17:12: warning: variable 'objective' set but not used [-Wunused-but-set-variable]
+    // double objective = result.Objective;
+
     this->P.Init = 'u';
 
     bool foundbetter = false;
@@ -26,7 +36,7 @@ FitResult<T> CDL012Swaps<T>::_Fit() {
         foundbetter = false;
 
         // TODO: shuffle NNz Indices to prevent bias.
-        //std::shuffle(std::begin(Order), std::end(Order), engine);
+        // std::shuffle(std::begin(Order), std::end(Order), engine);
 
         // TODO: This calculation is already preformed in a previous step
         // Can be pulled/stored
@@ -79,7 +89,9 @@ FitResult<T> CDL012Swaps<T>::_Fit() {
                 // Rcpp::Rcout << "Swap Objective  " <<  result.Objective << " \n";
                 // Rcpp::Rcout << "Old Objective  " <<  objective << " \n";
                 this->B = result.B;
-                objective = result.Objective;
+
+                // objective = result.Objective;
+
                 foundbetter = true;
                 break;
             }

diff --git a/src/DT2Matrix.cpp b/src/DT2Matrix.cpp
@@ -1,4 +1,5 @@
 #include <Rcpp.h>
+
 using namespace Rcpp;
 
 // [[Rcpp::export]]
@@ -32,16 +33,6 @@ NumericMatrix DT2Matrix(DataFrame weightDT) {
 // #' @return Weight matrix
 // #' @export
 // #'
-// #' @examples
-// #' Rcpp::sourceCpp("src/DT2Matrix.cpp")
-// #' library(inferCSN)
-// #' data("exampleMatrix")
-// #' weightDT <- inferCSN(exampleMatrix, verbose = TRUE)
-// #' weightMatrix <- DT2Matrix(weightDT)
-// #' genes <- gtools::mixedsort(unique(c(weightDT$regulator, weightDT$target)))
-// #' weightMatrix <- weightMatrix[genes, genes]
-// #' weightMatrixR <- DT2MatrixR(weightDT)
-// #'
 // DT2MatrixR <- function(weightDT) {
 //   colnames(weightDT) <- c("regulator", "target", "weight")
 //   genes <- gtools::mixedsort(unique(c(weightDT$regulator, weightDT$target)))
@@ -57,3 +48,25 @@ NumericMatrix DT2Matrix(DataFrame weightDT) {
 //
 //   return(weightMatrix)
 // }
+//
+// DT2MatrixR2 <- function(weightDT) {
+//   weightMatrix <- reshape2::acast(weightDT, regulator ~ target)[genes, genes]
+//   weightMatrix[is.na(weightMatrix)] <- 0
+//   return(weightMatrix)
+// }
+//
+// #' @examples
+// Rcpp::sourceCpp("src/DT2Matrix.cpp")
+//   library(inferCSN)
+//   data("exampleMatrix")
+//   weightDT <- inferCSN(exampleMatrix, verbose = TRUE)
+//   weightMatrix <- DT2Matrix(weightDT)
+//   genes <- gtools::mixedsort(unique(c(weightDT$regulator, weightDT$target)))
+//   weightMatrix <- weightMatrix[genes, genes]
+// weightMatrixR <- DT2MatrixR(weightDT)
+//   weightMatrixR2 <- DT2MatrixR2(weightDT)
+//
+// # Using `bench` package to evaluate the two versions of this function
+//   bench::mark(DT2MatrixR(weightDT),
+//               DT2Matrix(weightDT)[genes, genes],
+//                                  DT2MatrixR2(weightDT))
diff --git a/src/Grid1D.cpp b/src/Grid1D.cpp
@@ -191,12 +191,21 @@ std::vector<std::unique_ptr<FitResult<T>>> Grid1D<T>::Fit() {
 
                     std::vector<std::size_t> Spnew = nnzIndicies(result->B);
 
-                    bool samesupp = false;
-
-                    if (Spold == Spnew) {
-                        samesupp = true;
-                        scaledown = true;
-                    }
+                    // Remove the following 5 lines to emilate warning:
+                        // Grid1D.cpp: In instantiation of 'std::vector<std::unique_ptr<FitResult<T> > > Grid1D<T>::Fit() [with T = arma::Mat<double>]':
+                        // Grid1D.cpp:234:16:   required from here
+                        // Grid1D.cpp:194:26: warning: variable 'samesupp' set but not used [-Wunused-but-set-variable]
+                        //     194 |                     bool samesupp = false;
+                        //         |                          ^~~~~~~~
+                        // Grid1D.cpp: In instantiation of 'std::vector<std::unique_ptr<FitResult<T> > > Grid1D<T>::Fit() [with T = arma::SpMat<double>]':
+                        // Grid1D.cpp:235:16:   required from here
+                        // Grid1D.cpp:194:26: warning: variable 'samesupp' set but not used [-Wunused-but-set-variable]
+                    // bool samesupp = false;
+
+                    // if (Spold == Spnew) {
+                    //     samesupp = true;
+                    //     scaledown = true;
+                    // }
 
                     // if (samesupp) {
                     //     scaledown = true;

diff --git a/src/include/BetaVector.h b/src/include/BetaVector.h
@@ -7,7 +7,6 @@
  * arma::vec implementation
  */
 
-
 using beta_vector = arma::vec;
 //using beta_vector = arma::sp_mat;