[r] add row/col max stat functions

r/NAMESPACE

@@ -21,6 +21,9 @@ export(chrNames)
 export(cluster_graph_leiden)
 export(cluster_graph_louvain)
 export(cluster_graph_seurat)
+export(colMaxs)
+export(colMaxs.IterableMatrix)
+export(colMaxs.default)
 export(colMeans)
 export(colSums)
 export(colVars)
@@ -84,6 +87,9 @@ export(read_gencode_transcripts)
 export(read_gtf)
 export(read_ucsc_chrom_sizes)
 export(rotate_x_labels)
+export(rowMaxs)
+export(rowMaxs.IterableMatrix)
+export(rowMaxs.default)
 export(rowMeans)
 export(rowSums)
 export(rowVars)

r/NEWS.md

@@ -12,6 +12,9 @@ Contributions welcome :)
 - `apply_by_col()` and `apply_by_row()` allow providing custom R functions to compute per row/col summaries.
   In initial tests calculating row/col means using R functions is ~2x slower than the C++-based implementation but memory
   usage remains low.
+- Add `rowMaxs()` and `colMaxs()` functions, which return the maximum value in each row or column of a matrix. 
+  If `matrixStats` or `MatrixGenerics` packages are installed, `BPCells::rowMaxs()` will fall back to their implementations for non-BPCells objects.
+  Thanks to @immanuelazn for their first contribution as a new lab hire!
 
 ## Bug-fixes
 - Fixed error message when a matrix is too large to be converted to dgCMatrix (Thanks to @RookieA1 for reporting issue #95)

r/R/RcppExports.R

@@ -729,6 +729,14 @@ apply_matrix_double_cpp <- function(mat_sexp, f, row_major) {
     .Call(`_BPCells_apply_matrix_double_cpp`, mat_sexp, f, row_major)
 }
 
+matrix_max_per_row_cpp <- function(matrix) {
+    .Call(`_BPCells_matrix_max_per_row_cpp`, matrix)
+}
+
+matrix_max_per_col_cpp <- function(matrix) {
+    .Call(`_BPCells_matrix_max_per_col_cpp`, matrix)
+}
+
 matrix_identical_uint32_t_cpp <- function(mat1, mat2) {
     .Call(`_BPCells_matrix_identical_uint32_t_cpp`, mat1, mat2)
 }

r/R/matrix.R

@@ -27,7 +27,6 @@ setClass("IterableMatrix",
   )
 )
 
-
 #' Construct an S4 matrix object wrapping another matrix object
 #'
 #' Helps to avoid duplicate storage of dimnames
@@ -647,6 +646,78 @@ rlang::on_load({
   }
 })
 
+#' Get the max of each row in an iterable matrix
+#' @param x IterableMatrix object/dgCMatrix object
+#' @return * `rowMaxs()`: vector of maxes for every row
+#' @describeIn IterableMatrix-methods Calculate rowMaxs (replacement for `matrixStats::rowMaxs()`)
+#' @export
+rowMaxs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) UseMethod("rowMaxs")
+#' @export
+rowMaxs.default <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
+  if (requireNamespace("MatrixGenerics", quietly = TRUE)) {
+    MatrixGenerics::rowMaxs(x, rows = rows, cols = cols, na.rm = na.rm, ...)
+  } else if (requireNamespace("matrixStats", quietly = TRUE)) {
+    matrixStats::rowMaxs(x, rows = rows, cols = cols, na.rm = na.rm, ...)
+  }
+  else {
+    stop("Can't run rowMaxs on a non-BPCells object unless MatrixGenerics or matrixStats are installed.")
+  }
+}
+#' @export
+rowMaxs.IterableMatrix <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
+  if(!is.null(rows) || !is.null(cols) || !isFALSE(na.rm)) {
+    stop("rowMaxs(IterableMatrix) doesn't support extra arguments rows, cols, or na.rm")
+  }
+  iter <- iterate_matrix(convert_matrix_type(x, "double"))
+  if(x@transpose == TRUE) {
+    res <- matrix_max_per_col_cpp(iter)
+  } else {
+    res <- matrix_max_per_row_cpp(iter)
+  }
+  names(res) <- rownames(x)
+  return(res)
+}
+rlang::on_load({
+  if (requireNamespace("MatrixGenerics", quietly=TRUE)) {
+    setMethod(MatrixGenerics::rowMaxs, "IterableMatrix", rowMaxs.IterableMatrix)
+  }
+})
+
+#' Get the max of each col in an interable matrix
+#' @param x IterableMatrix/dgCMatrix object
+#' @return * `colMaxs()`: vector of column maxes
+#' @describeIn IterableMatrix-methods Calculate colMax (replacement for `matrixStats::colMax()`)
+#' @export
+colMaxs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) UseMethod("colMaxs")
+#' @export
+colMaxs.default <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
+  if (requireNamespace("MatrixGenerics", quietly = TRUE)) {
+    MatrixGenerics::colMaxs(x, rows = rows, cols = cols, na.rm = na.rm, ...)
+  } else if (requireNamespace("matrixStats", quietly = TRUE)) {
+    matrixStats::colMaxs(x, rows = rows, cols = cols, na.rm = na.rm, ...)
+  }
+  else {
+    stop("Can't run colMaxs on a non-BPCells object unless MatrixGenerics or matrixStats are installed.")
+  }
+}
+#' @export
+colMaxs.IterableMatrix <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
+  iter <- iterate_matrix(convert_matrix_type(x, "double"))
+  if(x@transpose == TRUE) {
+    res <- matrix_max_per_row_cpp(iter)
+  } else {
+    res <- matrix_max_per_col_cpp(iter)
+  }
+  names(res) <- colnames(x)
+  return(res)
+}
+rlang::on_load({
+  if (requireNamespace("MatrixGenerics", quietly=TRUE)) {
+    setMethod(MatrixGenerics::colMaxs, "IterableMatrix", colMaxs.IterableMatrix)
+  }
+})
+
+
 # Index subsetting
 setClass("MatrixSubset",
   contains = "IterableMatrix",

r/src/RcppExports.cpp

@@ -2418,6 +2418,28 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// matrix_max_per_row_cpp
+NumericVector matrix_max_per_row_cpp(SEXP matrix);
+RcppExport SEXP _BPCells_matrix_max_per_row_cpp(SEXP matrixSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< SEXP >::type matrix(matrixSEXP);
+    rcpp_result_gen = Rcpp::wrap(matrix_max_per_row_cpp(matrix));
+    return rcpp_result_gen;
+END_RCPP
+}
+// matrix_max_per_col_cpp
+NumericVector matrix_max_per_col_cpp(SEXP matrix);
+RcppExport SEXP _BPCells_matrix_max_per_col_cpp(SEXP matrixSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< SEXP >::type matrix(matrixSEXP);
+    rcpp_result_gen = Rcpp::wrap(matrix_max_per_col_cpp(matrix));
+    return rcpp_result_gen;
+END_RCPP
+}
 // matrix_identical_uint32_t_cpp
 bool matrix_identical_uint32_t_cpp(SEXP mat1, SEXP mat2);
 RcppExport SEXP _BPCells_matrix_identical_uint32_t_cpp(SEXP mat1SEXP, SEXP mat2SEXP) {
@@ -2614,6 +2636,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"_BPCells_matrix_value_histogram_cpp", (DL_FUNC) &_BPCells_matrix_value_histogram_cpp, 2},
     {"_BPCells_checksum_double_cpp", (DL_FUNC) &_BPCells_checksum_double_cpp, 1},
     {"_BPCells_apply_matrix_double_cpp", (DL_FUNC) &_BPCells_apply_matrix_double_cpp, 3},
+    {"_BPCells_matrix_max_per_row_cpp", (DL_FUNC) &_BPCells_matrix_max_per_row_cpp, 1},
+    {"_BPCells_matrix_max_per_col_cpp", (DL_FUNC) &_BPCells_matrix_max_per_col_cpp, 1},
     {"_BPCells_matrix_identical_uint32_t_cpp", (DL_FUNC) &_BPCells_matrix_identical_uint32_t_cpp, 2},
     {NULL, NULL, 0}
 };

r/src/matrix_utils.cpp

@@ -24,7 +24,6 @@
 #include "bpcells-cpp/matrixIterators/SVD.h"
 #include "bpcells-cpp/matrixIterators/TSparseMatrixWriter.h"
 #include "bpcells-cpp/matrixUtils/WilcoxonRankSum.h"
-
 #include "R_array_io.h"
 #include "R_interrupts.h"
 #include "R_xptr_wrapper.h"
@@ -624,6 +623,52 @@ List apply_matrix_double_cpp(SEXP mat_sexp, Function f, bool row_major) {
     return ret;
 }
 
+// Compute the max of each row
+// [[Rcpp::export]]
+NumericVector matrix_max_per_row_cpp(SEXP matrix) {
+    MatrixIterator<double> it(take_unique_xptr<MatrixLoader<double>>(matrix));
+    std::vector<double> result(it.rows());
+    std::vector<uint32_t> row_count(it.rows(), 0);
+    std::fill(result.begin(), result.end(), -INFINITY);
+    // keep track of the number of times we've seen each row
+    while (it.nextCol()) {
+        while (it.nextValue()) {
+            result[it.row()] = std::max(result[it.row()], it.val());
+            row_count[it.row()]++;
+    }}
+    // If we've seen a row less than the num of cols, we know there's at least one 0
+    for (size_t i = 0; i < it.rows(); i++) {
+        if (row_count[i] < it.cols()) {
+            result[i] = std::max(0.0, result[i]);
+        }
+    }
+    return Rcpp::wrap(result);
+}
+
+
+// Compute the max of each col
+// [[Rcpp::export]]
+NumericVector matrix_max_per_col_cpp(SEXP matrix) {
+    MatrixIterator<double> it(take_unique_xptr<MatrixLoader<double>>(matrix));
+    std::vector<double> result(it.cols(), -INFINITY);
+    // std::fill(result.begin(), result.end(), 0);
+    // keep track of the number of times we've seen each col
+    std::vector<uint32_t> col_count(it.cols(), 0);
+    while (it.nextCol()) {
+        while (it.nextValue()) {
+            result[it.col()] = std::max(result[it.col()], it.val());
+            col_count[it.col()]++;
+    }}
+    // If we've seen a col less than the num of rows, we know there's at least one 0
+    for (size_t i = 0; i < it.cols(); i++) {
+        if (col_count[i] < it.rows()) {
+            result[i] = std::max(0.0, result[i]);
+        }
+    }
+    return Rcpp::wrap(result);
+}
+
+
 // [[Rcpp::export]]
 bool matrix_identical_uint32_t_cpp(SEXP mat1, SEXP mat2) {
     MatrixIterator<uint32_t> i1(take_unique_xptr<MatrixLoader<uint32_t>>(mat1));

r/tests/testthat/test-matrix_stats.R

@@ -187,4 +187,24 @@ test_that("svds registers generic with RSpectra", {
   # Ensure RSpectra works with BPCells and BPCells works with RSpectra
   equal_svds(ans, RSpectra::svds(i1, k=5))
   equal_svds(ans, BPCells::svds(m1, k=5))
-})
+})
+
+test_that("rowMaxs and colMaxs works comprehensive", {
+  withr::local_seed(195123)
+  m1_neg <- matrix(runif(12, min = -10, max = -1), nrow = 3, ncol = 4)
+  m2_dense <- generate_dense_matrix(4, 64)
+  # Make a sparse matrix with half positive and half negative values
+  m3_sparse <- generate_sparse_matrix(4, 512)
+  m3_sparse@x <- m3_sparse@x * sample(c(-1,1), length(m3_sparse@x), replace=TRUE)
+
+  m_test_cases <- list(m1_neg, m2_dense, m3_sparse)
+  for (m in m_test_cases) {
+    i_transpose <- t(m) %>% as("dgCMatrix") %>% as("IterableMatrix")
+    i <- m %>% as("dgCMatrix") %>% as("IterableMatrix")
+    m_tranpose_cases <- list(i_transpose, t(i_transpose), i, t(i))
+    for (i in m_tranpose_cases) {
+      expect_identical(rowMaxs(i), matrixStats::rowMaxs(as.matrix(i)))
+      expect_identical(colMaxs(i), matrixStats::colMaxs(as.matrix(i)))
+    }
+  }
+})