fixed small issues (fb74885d) · Commits · github_fork / Scplot

.gitignore

0 → 100644

+1 −0

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		gh-pages

+6 −0

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		@@ -43,3 +43,9 @@ clean:
		cd ..;\
		$(RM) -r $(PKGNAME).Rcheck/

		pages:
		Rscript -e 'rmarkdown::render("gh-pages/index.Rmd")'

		publish:
		cd gh-pages;\
		git add .; git commit -m 'update'; git push

+7 −2

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		@@ -3,15 +3,20 @@
		##' @param object Seurat object
		##' @param features selected features (i.e., genes)
		##' @param dims selected dimensions (must be a two-length vector) that are used in visualization
		##' @param ncol number of facet columns if 'length(features) > 1'
		##' @param .fun user defined function that will be applied to selected features (default is to filter out genes with no expression values)
		##' @param ... additional parameters pass to 'scattermore::geom_scattermore()'
		##' @return layer of points for selected features
		##' @export
		sc_dim_geom_feature <- function(object, features, dims = c(1,2), ...,
		sc_dim_geom_feature <- function(object, features, dims = c(1,2), ncol=3, ...,
		.fun=function(.data) dplyr::filter(.data, .data$value > 0)) {
		d <- get_dim_data(object, dims=dims, features=features)
		d <- tidyr::pivot_longer(d, 4:ncol(d), names_to = "features")
		sc_geom_point(data = .fun(d), ...)
		d$features <- factor(d$features, levels = features)
		p <- sc_geom_point(data = .fun(d), ...)
		list(p,
		.feature_setting(features=features, ncol=ncol)
		)
		}

+14 −11

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		@@ -20,7 +20,7 @@
		##' @export
		sc_feature <- function(object, features,
		dims=c(1,2), reduction=NULL,
		cells=NULL, slot = "data", mapping, ncol=3, ...) {
		cells=NULL, slot = "data", mapping=NULL, ncol=3, ...) {
		d <- get_dim_data(object = object, features = features,
		dims = dims, reduction = reduction,
		cells = cells, slot = slot)
		@@ -39,23 +39,26 @@ sc_feature <- function(object, features,
		scale_color_gradient(low='grey', high='blue')
		#scale_color_gradient2(low='blue', mid='grey', high='red') +

		p + .feature_setting(features=features, ncol=ncol)
		}


		.feature_setting <- function(features, ncol) {
		if (length(features) == 1) {
		p <- p + ggtitle(features) +
		res <- list(ggtitle(features),
		theme(plot.title=element_text(size=rel(1.5), face='bold'))
		)
		} else {
		p <- p + facet_wrap(~features, ncol=ncol) +
		theme_bw()
		res <- list(facet_wrap(~features, ncol=ncol),
		theme_bw(),
		theme(axis.text = element_blank(),
		axis.title = element_blank(),
		axis.ticks = element_blank(),
		panel.grid = element_blank()
		)
		)
		}

		return(p)
		return(res)
		}

		## features = c("MS4A1", "GNLY", "CD3E", "CD14", "FCER1A", "FCGR3A", "LYZ", "PPBP", "CD8A")
		## sc_feature(pbmc, features)

+1 −0

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		@@ -23,6 +23,7 @@ sc_violin <- function(object, features,
		mapping = NULL, ncol=3, ...) {
		d <- get_dim_data(object, dims=NULL, features=features)
		d <- tidyr::pivot_longer(d, 2:ncol(d), names_to = "features")
		d$features <- factor(d$features, levels = features)
		if (!is.null(.fun)) {
		d <- .fun(d)
		}