diff --git a/DESCRIPTION b/DESCRIPTION index f0c057dc..7e40c269 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,7 @@ Description: Provides classes and functions for quality control, number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available. -License: Apache License 2.0 | file LICENSE +License: Apache License 2.0 URL: https://github.com/insightsengineering/hermes/ BugReports: https://github.com/insightsengineering/hermes/issues Depends: diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 63aaf2de..00000000 --- a/LICENSE +++ /dev/null @@ -1,13 +0,0 @@ -Copyright 2022 F. Hoffmann-La Roche AG - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. diff --git a/NAMESPACE b/NAMESPACE index d0ae9466..da57fd73 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -118,17 +118,17 @@ import(ggplot2) import(methods) importClassesFrom(biomaRt,Mart) importFrom(Biobase,samples) -importFrom(BiocGenerics,`annotation<-`) -importFrom(BiocGenerics,`counts<-`) +importFrom(BiocGenerics,"annotation<-") +importFrom(BiocGenerics,"counts<-") importFrom(BiocGenerics,annotation) importFrom(BiocGenerics,counts) importFrom(BiocGenerics,normalize) importFrom(ComplexHeatmap,add_heatmap) importFrom(R6,is.R6) importFrom(Rdpack,append_to_Rd_list) -importFrom(S4Vectors,`metadata<-`) -importFrom(S4Vectors,`rename`) +importFrom(S4Vectors,"metadata<-") importFrom(S4Vectors,isEmpty) +importFrom(S4Vectors,rename) importFrom(circlize,add_transparency) importFrom(dplyr,mutate) importFrom(forcats,as_factor) diff --git a/R/HermesData-methods.R b/R/HermesData-methods.R index 169f11d5..ad80e94e 100644 --- a/R/HermesData-methods.R +++ b/R/HermesData-methods.R @@ -81,7 +81,7 @@ NULL #' @param value (`list`)\cr the list to replace the current metadata with. #' #' @return The metadata which is a list. -#' @importFrom S4Vectors `metadata<-` +#' @importFrom S4Vectors metadata<- #' @importMethodsFrom S4Vectors metadata #' @exportMethod metadata #' @export `metadata<-` @@ -146,7 +146,7 @@ setMethod( #' that additional annotations beyond the required ones may be supplied and #' will be stored. #' -#' @importFrom BiocGenerics `annotation<-` +#' @importFrom BiocGenerics annotation<- #' @rdname annotation #' @export setReplaceMethod( @@ -188,6 +188,7 @@ setReplaceMethod( #' #' @param object (`AnyHermesData`)\cr object to access the counts from. #' @param value (`matrix`)\cr what should the counts assay be replaced with. +#' @param ... not used. #' #' @return The counts assay. #' @@ -202,7 +203,7 @@ setReplaceMethod( setMethod( f = "counts", signature = "AnyHermesData", - definition = function(object) { + definition = function(object, ...) { assay(object) } ) @@ -214,7 +215,7 @@ setMethod( #' are not identical to the `dimnames` on the `AnyHermesData` object; #' it does not influence actual assignment of `dimnames` to the assay #' (they're always stored as-is). -#' @importFrom BiocGenerics `counts<-` +#' @importFrom BiocGenerics counts<- #' @export #' #' @examples @@ -223,7 +224,7 @@ setMethod( setReplaceMethod( f = "counts", signature = signature(object = "AnyHermesData", value = "matrix"), - definition = function(object, value, withDimnames = TRUE) { + definition = function(object, ..., withDimnames = TRUE, value) { assay(object, withDimnames = withDimnames) <- value validObject(object) object @@ -581,7 +582,7 @@ h_map_pos <- function(names, map) { #' #' @return The [`SummarizedExperiment::SummarizedExperiment`] object with renamed contents. #' -#' @importFrom S4Vectors `rename` +#' @importFrom S4Vectors rename #' @export #' @examples #' x <- summarized_experiment diff --git a/man/counts.Rd b/man/counts.Rd index b242b045..ee0dcd2c 100644 --- a/man/counts.Rd +++ b/man/counts.Rd @@ -6,20 +6,22 @@ \alias{counts<-,AnyHermesData,matrix-method} \title{Counts Accessor and Setter} \usage{ -\S4method{counts}{AnyHermesData}(object) +\S4method{counts}{AnyHermesData}(object, ...) -\S4method{counts}{AnyHermesData,matrix}(object, withDimnames = TRUE) <- value +\S4method{counts}{AnyHermesData,matrix}(object, ..., withDimnames = TRUE) <- value } \arguments{ \item{object}{(\code{AnyHermesData})\cr object to access the counts from.} -\item{value}{(\code{matrix})\cr what should the counts assay be replaced with.} +\item{...}{not used.} \item{withDimnames}{(\code{flag})\cr setting \code{withDimnames =FALSE} in the setter (\verb{counts<-}) is required when the \code{dimnames} on the supplied counts assay are not identical to the \code{dimnames} on the \code{AnyHermesData} object; it does not influence actual assignment of \code{dimnames} to the assay (they're always stored as-is).} + +\item{value}{(\code{matrix})\cr what should the counts assay be replaced with.} } \value{ The counts assay. diff --git a/tests/testthat/_snaps/draw_boxplot/draw-boxplot-with-duplicate-labels.svg b/tests/testthat/_snaps/draw_boxplot/draw-boxplot-with-duplicate-labels.svg index 4ec6078b..4e752c2a 100644 --- a/tests/testthat/_snaps/draw_boxplot/draw-boxplot-with-duplicate-labels.svg +++ b/tests/testthat/_snaps/draw_boxplot/draw-boxplot-with-duplicate-labels.svg @@ -27,14 +27,14 @@ - - - - - + + + + + - - + + diff --git a/tests/testthat/_snaps/graphs/draw-libsize-densities-with-default-log.svg b/tests/testthat/_snaps/graphs/draw-libsize-densities-with-default-log.svg index c555fae6..f6faba67 100644 --- a/tests/testthat/_snaps/graphs/draw-libsize-densities-with-default-log.svg +++ b/tests/testthat/_snaps/graphs/draw-libsize-densities-with-default-log.svg @@ -27,55 +27,55 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 0.1 -0.2 +0.2 - - + +