diff --git a/DESCRIPTION b/DESCRIPTION index 2aa583e..6f41952 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,44 +33,46 @@ Encoding: UTF-8 LazyData: false Depends: R (>= 4.0), - SummarizedExperiment, - TreeSummarizedExperiment, - mia (>= 1.13.0), ggplot2, - ggraph (>= 2.0) + ggraph (>= 2.0), + mia (>= 1.13.0), + SummarizedExperiment, + TreeSummarizedExperiment Imports: - methods, - stats, - S4Vectors, + ape, BiocGenerics, BiocParallel, DelayedArray, - scater, - ggtree, + DirichletMultinomial, + dplyr, + ggh4x, ggnewscale, - viridis, + ggrepel, + ggplot2, + ggraph, + ggtree, + methods, + rlang, + scater, + S4Vectors, + SingleCellExperiment, + stats, tibble, - tidytext, - tidytree, tidygraph, - rlang, - purrr, tidyr, - dplyr, - ape, - DirichletMultinomial, - ggrepel, - SingleCellExperiment + tidytext, + tidytree, + viridis Suggests: - knitr, - rmarkdown, BiocStyle, - testthat, - patchwork, - vegan, bluster, + circlize, ComplexHeatmap, - circlize + knitr, + patchwork, + rmarkdown, + testthat, + vegan Remotes: github::microbiome/miaTime Roxygen: list(markdown = TRUE) diff --git a/NAMESPACE b/NAMESPACE index 3732072..ed3d555 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -86,6 +86,7 @@ importFrom(dplyr,select) importFrom(dplyr,summarise) importFrom(dplyr,summarize) importFrom(dplyr,ungroup) +importFrom(ggh4x,facet_nested) importFrom(ggnewscale,new_scale) importFrom(ggnewscale,new_scale_colour) importFrom(ggnewscale,new_scale_fill) diff --git a/R/plotAbundance.R b/R/plotAbundance.R index 3b7971a..6d4c58c 100644 --- a/R/plotAbundance.R +++ b/R/plotAbundance.R @@ -546,6 +546,7 @@ setMethod("plotAbundance", signature = c("SummarizedExperiment"), function( # to split rows to unique facets. #' @importFrom dplyr select all_of distinct arrange select #' @importFrom stats formula +#' @importFrom ggh4x facet_nested .abund_plotter_incorporate_metadata <- function( plot_out, df, col.var = features, features = NULL, facet.cols = FALSE, facet.rows = one.facet,