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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| #' Clip outliers | ||
| #' | ||
| #' Clip outliers from a ggplot object using Mahalanobis distance. | ||
| #' @param gg A ggplot or patchwork object. | ||
| #' @param max_dist Maximum Mahalanobis distance to consider as a non-outlier. | ||
| #' @inheritParams patchwork::plot_layout | ||
| #' @inheritDotParams patchwork::wrap_plots | ||
| #' @return A ggplot or patchwork object with outliers clipped. | ||
| #' @export | ||
| #' @examples | ||
| #' gg <- ggplot2::ggplot(mtcars,ggplot2::aes(x=mpg,y=disp))+ggplot2::geom_point() | ||
| #' clip_outliers(gg) | ||
| clip_outliers <- function(gg, | ||
| max_dist=NULL, | ||
| guides = "collect", | ||
| axes="collect", | ||
| axis_titles="collect", | ||
| ...){ | ||
|
|
||
| if(isFALSE(max_dist)) return(gg) | ||
|
|
||
| clip_outliers_i <- function(gg, max_dist){ | ||
| is.outlier <- mahal.dist <- NULL; | ||
|
|
||
| df <- ggplot2::ggplot_build(gg)$data[[1]][,c("x","y")] | ||
| outlier_md <- rstatix::mahalanobis_distance(data.table::data.table(df)) | ||
| if(!is.null(max_dist)){ | ||
| outlier_md[,is.outlier:=mahal.dist>max_dist] | ||
| } | ||
| messager(formatC(sum(outlier_md$is.outlier),big.mark=","), | ||
| "outliers identified.") | ||
| messager("max_dist for non-outlier:", | ||
| max(outlier_md[is.outlier==FALSE,]$mahal.dist)) | ||
| # ggplot(aes(x,y),data = outlier_md)+ | ||
| # geom_point(aes(color=factor(is.outlier)),size=5) | ||
| gg + | ||
| ggplot2::lims(x=c(min(outlier_md[is.outlier==FALSE]$x), | ||
| max(outlier_md[is.outlier==FALSE]$x) | ||
| ), | ||
| y=c(min(outlier_md[is.outlier==FALSE]$y), | ||
| max(outlier_md[is.outlier==FALSE]$y) | ||
| ) | ||
| ) | ||
| } | ||
| if(methods::is(gg,"patchwork")){ | ||
| lapply(seq(length(gg)), function(i){ | ||
| clip_outliers_i(gg[[i]],max_dist) | ||
| }) |> | ||
| patchwork::wrap_plots(...) + | ||
| patchwork::plot_layout(guides = guides, | ||
| axes = axes, | ||
| axis_titles =axis_titles) | ||
| } else{ | ||
| clip_outliers_i(gg,max_dist) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| #' Plot ontological similarity | ||
| #' | ||
| #' Plot ontological similarity of cells to a set of terms in an ontology. | ||
| #' @inheritDotParams Seurat::FeaturePlot | ||
| #' @export | ||
| plot_ontological_similarity <- function(obj, | ||
| id_col, | ||
| ont, | ||
| ### Use pre-computed DOSA results | ||
| run_ontological_similarity_out=NULL, | ||
| ### Args for running new DOSA | ||
| ancestors=unique(ont@elementMetadata$ancestor), | ||
| group_var="seurat_clusters", | ||
| top_n=9, | ||
| min.cutoff = "q90", | ||
| show_plot=TRUE, | ||
| ...){ | ||
| if(!is.null(run_ontological_similarity_out)){ | ||
| messager("Using pre-computed DOSA results.") | ||
| out <- run_ontological_similarity_out | ||
| } else { | ||
| out <- run_ontological_similarity( | ||
| obj=obj, | ||
| id_col=id_col, | ||
| ont=ont, | ||
| ancestors=ancestors, | ||
| group_var=group_var) | ||
| } | ||
| #### Plot most differentially similar ancestors #### | ||
| terms_to_use <- if(length(out$top_markers)==0){ | ||
| messager("No term identified from DOSA. Using ancestors instead.") | ||
| intersect(ancestors,colnames(out$sim)) | ||
| } else { | ||
| unique(out$top_markers) | ||
| } | ||
| term_map <- KGExplorer::map_ontology_terms(ont = ont, | ||
| keep_order = FALSE, | ||
| terms = terms_to_use)|> | ||
| utils::head(top_n) | ||
| term_map <- term_map[!is.na(names(term_map))] | ||
| ### Order ancestors by their clustered similarity | ||
| d <- stats::dist(out$sim[names(term_map),]) | ||
| hc <- stats::hclust(d) | ||
| term_map <- term_map[hc$labels[hc$order]] | ||
|
|
||
| fo <- Seurat::FeaturePlot(out$obj_sim, | ||
| order = TRUE, | ||
| min.cutoff = min.cutoff, | ||
| features = names(term_map), | ||
| ...) | ||
| fig_ontmarkers <- lapply(seq(length(term_map)), function(i){ | ||
| fo_i <- fo[[i]] + | ||
| ggplot2::labs(title=NULL, | ||
| subtitle=paste(term_map[[i]], | ||
| names(term_map)[[i]],sep="\n"), | ||
| color="Ontological\nsimilarity" | ||
| )+ | ||
| phenomix::theme_nightlight() + | ||
| phenomix::scale_color_nightlight() | ||
| if(i>1){ | ||
| fo_i <- fo_i + ggplot2::theme(legend.position = "none") | ||
| } | ||
| fo_i | ||
| })|>patchwork::wrap_plots() + | ||
| patchwork::plot_layout(axes = "collect", | ||
| axis_titles = "collect", | ||
| guides = "collect" | ||
| ) | ||
|
|
||
| if(isTRUE(show_plot)) methods::show(fig_ontmarkers) | ||
| #### Return #### | ||
| return( | ||
| list(plot=fig_ontmarkers, | ||
| run_ontological_similarity=out, | ||
| hclust=hc, | ||
| term_map=term_map | ||
| ) | ||
| ) | ||
| } |
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