From cc60d4e8daba2ac835feea9460e9f825fa2d48ee Mon Sep 17 00:00:00 2001 From: mgrasshoff Date: Thu, 3 Oct 2024 16:50:48 +0200 Subject: [PATCH] Fixing vignette building. --- DESCRIPTION | 2 +- R/ClonalDefinition.R | 4 +- R/LoadingMAEGATK_typewise.R | 2 +- _pkgdown.yml | 2 + docs/404.html | 3 +- docs/articles/BoneMarrow_SIGURD.html | 14 +++---- docs/articles/MPN_SIGURD.html | 3 +- docs/articles/SW_CellMixture_SIGURD.html | 3 +- docs/articles/TenX_CellMixture_SIGURD.html | 3 +- docs/articles/index.html | 7 +++- docs/authors.html | 7 ++-- docs/index.html | 6 +-- docs/pkgdown.yml | 3 +- docs/reference/AllelFrequencyFoldChange.html | 3 +- docs/reference/AmpliconSupplementing.html | 3 +- docs/reference/CalculateAlleleFrequency.html | 3 +- docs/reference/CalculateAltReads.html | 3 +- docs/reference/CalculateConsensus.html | 3 +- .../reference/CalculateCorrelationPValue.html | 3 +- docs/reference/CalculateCoverage.html | 3 +- docs/reference/CalculateFisherTestPValue.html | 3 +- docs/reference/CalculateQuality.html | 3 +- docs/reference/CalculateRefReads.html | 3 +- .../reference/CalculateStrandCorrelation.html | 3 +- docs/reference/CallSupport.html | 3 +- docs/reference/ClonalDefinition.html | 3 +- docs/reference/ClonalDiversity.html | 3 +- docs/reference/CombineSEobjects.html | 3 +- docs/reference/Enrichment_FisherTest.html | 3 +- docs/reference/Filtering.html | 3 +- docs/reference/GetCellInfoPerVariant.html | 3 +- docs/reference/GetVariantInfo.html | 3 +- docs/reference/HeatmapVoi.html | 3 +- docs/reference/LoadingMAEGATK_typewise.html | 3 +- docs/reference/LoadingVCF_typewise.html | 3 +- docs/reference/LoadingVarTrix_typewise.html | 3 +- docs/reference/Merging_SE_list.html | 3 +- docs/reference/RowWiseSplit.html | 3 +- docs/reference/SeparatingMatrixToList.html | 3 +- docs/reference/SetVariantInfo.html | 3 +- docs/reference/UMIQC.html | 3 +- docs/reference/UMI_seq.html | 3 +- docs/reference/VariantBurden.html | 3 +- .../VariantCloneSizeThresholding.html | 3 +- docs/reference/VariantCorrelationHeatmap.html | 3 +- docs/reference/VariantFisherTestHeatmap.html | 3 +- .../VariantQuantileThresholding_Combined.html | 3 +- docs/reference/VariantSelection_Group.html | 3 +- docs/reference/VariantSelection_Quantile.html | 3 +- docs/reference/VariantSelection_TopCells.html | 3 +- docs/reference/VariantWiseCorrelation.html | 3 +- docs/reference/VariantWiseFisherTest.html | 3 +- docs/reference/char_to_numeric.html | 3 +- docs/reference/combine_NAMES.html | 3 +- docs/reference/combine_SparseMatrix.html | 3 +- docs/reference/computeAFMutMatrix.html | 3 +- docs/reference/getAltMatrix.html | 3 +- docs/reference/getMutMatrix.html | 3 +- docs/reference/getReadMatrix.html | 3 +- docs/reference/getRefMatrix.html | 3 +- docs/reference/get_consensus.html | 3 +- docs/reference/index.html | 3 +- docs/reference/load_object.html | 3 +- docs/reference/save_object.html | 3 +- docs/reference/sdiv.html | 3 +- docs/search.json | 2 +- vignettes/BoneMarrow_SIGURD.Rmd | 2 +- vignettes/MPN_SIGURD.Rmd | 38 +++++++++++++++++++ 68 files changed, 179 insertions(+), 78 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 331e42e..4092f2e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,5 +53,5 @@ Suggests: testthat (>= 3.0.0), tidyr, tidyverse -VignetteBuilder: knitr +# VignetteBuilder: knitr Config/testthat/edition: 3 diff --git a/R/ClonalDefinition.R b/R/ClonalDefinition.R index 5de1a9b..30df9d0 100644 --- a/R/ClonalDefinition.R +++ b/R/ClonalDefinition.R @@ -11,10 +11,11 @@ #'@param se SummarizedExperiment object. #'@param variants_ls List of variants for clonal definition #'@param grouping The meta data column used to split the cells into groups. Default = NULL +#'@param n_cores Number of cores you want to use. Numeric. #'@param identities Vector of groups, like samples. #'@param verbose Should the function be verbose? Default = TRUE #'@export -ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL, verbose = TRUE){ +ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL, n_cores = 1, verbose = TRUE){ # Checking if the group variable is in the column data. if(!is.null(grouping)){ # We check if the grouping variable is in the column data. @@ -109,7 +110,6 @@ ClonalDefinition <- function(se, variants_ls, grouping = NULL, identities = NULL cells_rest <- rep(TRUE, ncol(se_use)) } cells <- colSums(rbind(cells, cells_rest)) == 2 - coverage <- mean(colMeans(SummarizedExperiment::assays(se_use)[["coverage"]][combination_use, cells, drop = FALSE])) cells <- cells[cells] new_meta_data_subset[names(cells)] <- paste0("C", combination_number) combinations_meta_data[[i]] <- rbind(combinations_meta_data[[i]], diff --git a/R/LoadingMAEGATK_typewise.R b/R/LoadingMAEGATK_typewise.R index 150886c..d43a878 100644 --- a/R/LoadingMAEGATK_typewise.R +++ b/R/LoadingMAEGATK_typewise.R @@ -26,7 +26,7 @@ #'@param cellbarcode_length The length of the cell barcode. This should be the length of the actual barcode plus two for the suffix (-1). Default = 18 #'@param verbose Should the function be verbose? Default = TRUE #'@export -LoadingMAEGATK_typewise <- function(samples_file, samples_path = NULL, patient, patient_column = "patient", type_use = "scRNAseq_MT", chromosome_prefix = "chrM", +LoadingMAEGATK_typewise <- function(samples_file, patient, samples_path = NULL, patient_column = "patient", type_use = "scRNAseq_MT", chromosome_prefix = "chrM", min_cells = 2, cells_include = NULL, cells_exclude = NULL, barcodes_path = NULL, cellbarcode_length = 18, verbose = TRUE){ if(all(!is.null(samples_path), !is.null(barcodes_path))){ if(verbose) print(paste0("Loading the data for patient ", patient, ".")) diff --git a/_pkgdown.yml b/_pkgdown.yml index fb62923..038cd27 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -3,3 +3,5 @@ template: bootstrap: 5 vignettes: build: false +build: + copy_vignettes: true diff --git a/docs/404.html b/docs/404.html index 7114001..28b326d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -24,7 +24,7 @@ sigurd - 0.2.61 + 0.3.0