tests/testthat/helper-globals.R

In acidgenomics/AcidPlots: Acid Genomics Plot Functions and Themes

## nolint start

## Fix for pheatmap partial match warning.
## https://github.com/raivokolde/pheatmap/issues/46
options(
    "warnPartialMatchAttr" = FALSE,
    "warnPartialMatchDollar" = FALSE
)

data <- utils::data

data(
    KnownMarkers,
    RangedSummarizedExperiment,
    SingleCellExperiment_Seurat,
    SingleCellExperiment_splatter,
    matrix,
    matrix_lfc,
    package = "AcidTest",
    envir = environment()
)

`assay<-` <- SummarizedExperiment::`assay<-`
`colData<-` <- SummarizedExperiment::`colData<-`
`rowData<-` <- SummarizedExperiment::`rowData<-`
allAreHexColors <- goalie::allAreHexColors
assay <- SummarizedExperiment::assay
calculateMetrics <- AcidGenerics::calculateMetrics
ggplot_build <- ggplot2::ggplot_build
import <- pipette::import
isInstalled <- goalie::isInstalled
mpg <- ggplot2::mpg
nonzeroRowsAndCols <- AcidGenerics::nonzeroRowsAndCols
rowData <- SummarizedExperiment::rowData
sampleNames <- Biobase::sampleNames

rse <- RangedSummarizedExperiment
sce <- SingleCellExperiment_splatter
object <- rse

rownames <- head(rownames(rse))
geneIds <- head(as.character(rowData(rse)[["geneId"]]))
geneNames <- head(as.character(rowData(rse)[["geneName"]]))
genes <- geneIds

## nolint end