Commit 57339319 authored by Ilya Korsunsky's avatar Ilya Korsunsky
Browse files

fixed bug in tidy_results function

parent 1681204e

DESCRIPTION

+1 −1
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ Authors@R: c( 
        role = c("aut"), comment = c(ORCID = "0000-0002-1901-8265"))

    )

Description: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment. 

License: GPL-3 + file LICENSE

License: GPL-3

Encoding: UTF-8

Depends: R (>= 3.4.0), Rcpp

LinkingTo: Rcpp, RcppArmadillo

R/RcppExports.R

+11 −11
Original line number Diff line number Diff line
@@ -2,46 +2,46 @@ 
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393



cpp_sumGroups_dgc <- function(x, p, i, ncol, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dgc', PACKAGE = 'presto', x, p, i, ncol, groups, ngroups)

    .Call('_Presto_cpp_sumGroups_dgc', PACKAGE = 'Presto', x, p, i, ncol, groups, ngroups)

}



cpp_sumGroups_dgc_T <- function(x, p, i, ncol, nrow, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dgc_T', PACKAGE = 'presto', x, p, i, ncol, nrow, groups, ngroups)

    .Call('_Presto_cpp_sumGroups_dgc_T', PACKAGE = 'Presto', x, p, i, ncol, nrow, groups, ngroups)

}



cpp_sumGroups_dense <- function(X, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dense', PACKAGE = 'presto', X, groups, ngroups)

    .Call('_Presto_cpp_sumGroups_dense', PACKAGE = 'Presto', X, groups, ngroups)

}



cpp_sumGroups_dense_T <- function(X, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dense_T', PACKAGE = 'presto', X, groups, ngroups)

    .Call('_Presto_cpp_sumGroups_dense_T', PACKAGE = 'Presto', X, groups, ngroups)

}



cpp_nnzeroGroups_dense <- function(X, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dense', PACKAGE = 'presto', X, groups, ngroups)

    .Call('_Presto_cpp_nnzeroGroups_dense', PACKAGE = 'Presto', X, groups, ngroups)

}



cpp_nnzeroGroups_dense_T <- function(X, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dense_T', PACKAGE = 'presto', X, groups, ngroups)

    .Call('_Presto_cpp_nnzeroGroups_dense_T', PACKAGE = 'Presto', X, groups, ngroups)

}



cpp_nnzeroGroups_dgc <- function(p, i, ncol, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dgc', PACKAGE = 'presto', p, i, ncol, groups, ngroups)

    .Call('_Presto_cpp_nnzeroGroups_dgc', PACKAGE = 'Presto', p, i, ncol, groups, ngroups)

}



cpp_in_place_rank_mean <- function(v_temp, idx_begin, idx_end) {

    .Call('_presto_cpp_in_place_rank_mean', PACKAGE = 'presto', v_temp, idx_begin, idx_end)

    .Call('_Presto_cpp_in_place_rank_mean', PACKAGE = 'Presto', v_temp, idx_begin, idx_end)

}



cpp_rank_matrix_dgc <- function(x, p, nrow, ncol) {

    .Call('_presto_cpp_rank_matrix_dgc', PACKAGE = 'presto', x, p, nrow, ncol)

    .Call('_Presto_cpp_rank_matrix_dgc', PACKAGE = 'Presto', x, p, nrow, ncol)

}



cpp_rank_matrix_dense <- function(X) {

    .Call('_presto_cpp_rank_matrix_dense', PACKAGE = 'presto', X)

    .Call('_Presto_cpp_rank_matrix_dense', PACKAGE = 'Presto', X)

}



cpp_nnzeroGroups_dgc_T <- function(p, i, ncol, nrow, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dgc_T', PACKAGE = 'presto', p, i, ncol, nrow, groups, ngroups)

    .Call('_Presto_cpp_nnzeroGroups_dgc_T', PACKAGE = 'Presto', p, i, ncol, nrow, groups, ngroups)

}

R/utils.R

+4 −4
Original line number Diff line number Diff line
@@ -16,9 +16,9 @@ NULL 
tidy_results <- function(wide_res, features, groups) {

    res <- Reduce(cbind, lapply(wide_res, as.numeric)) %>% data.frame() 

    colnames(res) <- names(wide_res)

    res$feature <- rep(features, length(groups))

    res$group <- rep(groups, length(features))

    res <- res %>% dplyr::select(

    res$feature <- rep(features, times = length(groups))

    res$group <- rep(groups, each = length(features))

    res %>% dplyr::select(

        .data$feature, 

        .data$group, 

        .data$avgExpr,

src/RcppExports.cpp

+23 −23
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ using namespace Rcpp; 


// cpp_sumGroups_dgc

arma::mat cpp_sumGroups_dgc(const arma::vec& x, const arma::uvec& p, const arma::vec& i, unsigned ncol, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_sumGroups_dgc(SEXP xSEXP, SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_sumGroups_dgc(SEXP xSEXP, SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -24,7 +24,7 @@ END_RCPP 
}

// cpp_sumGroups_dgc_T

arma::mat cpp_sumGroups_dgc_T(const arma::vec& x, const arma::vec& p, const arma::vec& i, int ncol, int nrow, const arma::uvec& groups, int ngroups);

RcppExport SEXP _presto_cpp_sumGroups_dgc_T(SEXP xSEXP, SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP nrowSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_sumGroups_dgc_T(SEXP xSEXP, SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP nrowSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -41,7 +41,7 @@ END_RCPP 
}

// cpp_sumGroups_dense

arma::mat cpp_sumGroups_dense(const arma::mat& X, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_sumGroups_dense(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_sumGroups_dense(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -54,7 +54,7 @@ END_RCPP 
}

// cpp_sumGroups_dense_T

arma::mat cpp_sumGroups_dense_T(const arma::mat& X, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_sumGroups_dense_T(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_sumGroups_dense_T(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -67,7 +67,7 @@ END_RCPP 
}

// cpp_nnzeroGroups_dense

arma::mat cpp_nnzeroGroups_dense(const arma::mat& X, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_nnzeroGroups_dense(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_nnzeroGroups_dense(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -80,7 +80,7 @@ END_RCPP 
}

// cpp_nnzeroGroups_dense_T

arma::mat cpp_nnzeroGroups_dense_T(const arma::mat& X, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_nnzeroGroups_dense_T(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_nnzeroGroups_dense_T(SEXP XSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -93,7 +93,7 @@ END_RCPP 
}

// cpp_nnzeroGroups_dgc

arma::mat cpp_nnzeroGroups_dgc(const arma::uvec& p, const arma::vec& i, unsigned ncol, const arma::uvec& groups, unsigned ngroups);

RcppExport SEXP _presto_cpp_nnzeroGroups_dgc(SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_nnzeroGroups_dgc(SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -108,7 +108,7 @@ END_RCPP 
}

// cpp_in_place_rank_mean

std::list<float> cpp_in_place_rank_mean(arma::vec& v_temp, int idx_begin, int idx_end);

RcppExport SEXP _presto_cpp_in_place_rank_mean(SEXP v_tempSEXP, SEXP idx_beginSEXP, SEXP idx_endSEXP) {

RcppExport SEXP _Presto_cpp_in_place_rank_mean(SEXP v_tempSEXP, SEXP idx_beginSEXP, SEXP idx_endSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -121,7 +121,7 @@ END_RCPP 
}

// cpp_rank_matrix_dgc

std::vector<std::list<float> > cpp_rank_matrix_dgc(arma::vec& x, const arma::vec& p, int nrow, int ncol);

RcppExport SEXP _presto_cpp_rank_matrix_dgc(SEXP xSEXP, SEXP pSEXP, SEXP nrowSEXP, SEXP ncolSEXP) {

RcppExport SEXP _Presto_cpp_rank_matrix_dgc(SEXP xSEXP, SEXP pSEXP, SEXP nrowSEXP, SEXP ncolSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -135,7 +135,7 @@ END_RCPP 
}

// cpp_rank_matrix_dense

Rcpp::List cpp_rank_matrix_dense(arma::mat& X);

RcppExport SEXP _presto_cpp_rank_matrix_dense(SEXP XSEXP) {

RcppExport SEXP _Presto_cpp_rank_matrix_dense(SEXP XSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -146,7 +146,7 @@ END_RCPP 
}

// cpp_nnzeroGroups_dgc_T

arma::mat cpp_nnzeroGroups_dgc_T(const arma::vec& p, const arma::vec& i, int ncol, int nrow, const arma::uvec& groups, int ngroups);

RcppExport SEXP _presto_cpp_nnzeroGroups_dgc_T(SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP nrowSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

RcppExport SEXP _Presto_cpp_nnzeroGroups_dgc_T(SEXP pSEXP, SEXP iSEXP, SEXP ncolSEXP, SEXP nrowSEXP, SEXP groupsSEXP, SEXP ngroupsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;
@@ -162,21 +162,21 @@ END_RCPP 
}



static const R_CallMethodDef CallEntries[] = {

    {"_presto_cpp_sumGroups_dgc", (DL_FUNC) &_presto_cpp_sumGroups_dgc, 6},

    {"_presto_cpp_sumGroups_dgc_T", (DL_FUNC) &_presto_cpp_sumGroups_dgc_T, 7},

    {"_presto_cpp_sumGroups_dense", (DL_FUNC) &_presto_cpp_sumGroups_dense, 3},

    {"_presto_cpp_sumGroups_dense_T", (DL_FUNC) &_presto_cpp_sumGroups_dense_T, 3},

    {"_presto_cpp_nnzeroGroups_dense", (DL_FUNC) &_presto_cpp_nnzeroGroups_dense, 3},

    {"_presto_cpp_nnzeroGroups_dense_T", (DL_FUNC) &_presto_cpp_nnzeroGroups_dense_T, 3},

    {"_presto_cpp_nnzeroGroups_dgc", (DL_FUNC) &_presto_cpp_nnzeroGroups_dgc, 5},

    {"_presto_cpp_in_place_rank_mean", (DL_FUNC) &_presto_cpp_in_place_rank_mean, 3},

    {"_presto_cpp_rank_matrix_dgc", (DL_FUNC) &_presto_cpp_rank_matrix_dgc, 4},

    {"_presto_cpp_rank_matrix_dense", (DL_FUNC) &_presto_cpp_rank_matrix_dense, 1},

    {"_presto_cpp_nnzeroGroups_dgc_T", (DL_FUNC) &_presto_cpp_nnzeroGroups_dgc_T, 6},

    {"_Presto_cpp_sumGroups_dgc", (DL_FUNC) &_Presto_cpp_sumGroups_dgc, 6},

    {"_Presto_cpp_sumGroups_dgc_T", (DL_FUNC) &_Presto_cpp_sumGroups_dgc_T, 7},

    {"_Presto_cpp_sumGroups_dense", (DL_FUNC) &_Presto_cpp_sumGroups_dense, 3},

    {"_Presto_cpp_sumGroups_dense_T", (DL_FUNC) &_Presto_cpp_sumGroups_dense_T, 3},

    {"_Presto_cpp_nnzeroGroups_dense", (DL_FUNC) &_Presto_cpp_nnzeroGroups_dense, 3},

    {"_Presto_cpp_nnzeroGroups_dense_T", (DL_FUNC) &_Presto_cpp_nnzeroGroups_dense_T, 3},

    {"_Presto_cpp_nnzeroGroups_dgc", (DL_FUNC) &_Presto_cpp_nnzeroGroups_dgc, 5},

    {"_Presto_cpp_in_place_rank_mean", (DL_FUNC) &_Presto_cpp_in_place_rank_mean, 3},

    {"_Presto_cpp_rank_matrix_dgc", (DL_FUNC) &_Presto_cpp_rank_matrix_dgc, 4},

    {"_Presto_cpp_rank_matrix_dense", (DL_FUNC) &_Presto_cpp_rank_matrix_dense, 1},

    {"_Presto_cpp_nnzeroGroups_dgc_T", (DL_FUNC) &_Presto_cpp_nnzeroGroups_dgc_T, 6},

    {NULL, NULL, 0}

};



RcppExport void R_init_presto(DllInfo *dll) {

RcppExport void R_init_Presto(DllInfo *dll) {

    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);

    R_useDynamicSymbols(dll, FALSE);

}

tests/testthat.R

+2 −2
Original line number Diff line number Diff line 
library(testthat)

library(presto)

library(Presto)



test_check("presto")
 
test_check("Presto")

CRA Git | Maintained and supported by SUSTech CRA and CCSE