sc-feature

Package: scplot

Title: What the Package Does (One Line, Title Case)

Version: 0.0.0.9000

Authors@R: 

    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),

           comment = c(ORCID = "YOUR-ORCID-ID"))

Description: What the package does (one paragraph).

License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a

    license

Encoding: UTF-8

Roxygen: list(markdown = TRUE)

RoxygenNote: 7.2.1

# Generated by roxygen2: do not edit by hand

sc_feature <- function(object, features, 

                    dims=c(1,2), reduction=NULL, 

                    cells=NULL, slot = "data") {

    if (is.null(reduction)) {

        reduction <- SeuratObject::DefaultDimReduc(object)

    }

    if (is.null(cells)) {

        cells <- colnames(object)

    }

    dims <- paste0(SeuratObject::Key(object = object[[reduction]]), dims)

    d <- SeuratObject::FetchData(object, vars = c(dims, "ident", 

        features), cells = cells, slot = slot)

    d2 <- tidyr::pivot_longer(d, 4:ncol(d))

    d2$name <- factor(d2$name, features)

    ggplot(d2, aes_string(dims[1], dims[2])) + 

        scattermore::geom_scattermore(aes(color=value), 

                    pointsize=2, pixels = c(700, 700)) +

        facet_wrap(~name, ncol=3) + 

        #scale_color_gradient2(low='blue', mid='grey', high='red') + 

        theme_bw() +

        theme(axis.text = element_blank(), 

            axis.title = element_blank(), 

            axis.ticks = element_blank(), 

            panel.grid = element_blank()

        )

}

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

## sc_feature(pbmc, features)