Takes in a Seurat or cell_dat_set object, extracts UMAP dimensions and gene expression values. For Seurat, default assay is "RNA"; can be changed to if necessary. For cell_data_set, the assay parameter does nothing; the function extracts log and size-factor normalized counts which are similar but not identical to the Seurat "RNA" assay. If a vector of genes is supplied to gene_or_genes, a faceted plot will be generated. If a dataframe is supplied, an aggregated plot will be generated with a facet for each gene group. The dataframe must be of 2 colums: the first containing feature ids and the second containing grouping information. This is best generated using bb_rowmeta.
Usage
bb_gene_umap(
obj,
gene_or_genes,
assay = "RNA",
order = TRUE,
cell_size = 1,
alpha = 1,
ncol = NULL,
plot_title = NULL,
color_legend_title = "Expression",
max_expr_val = NULL,
alt_dim_x = NULL,
alt_dim_y = NULL,
rasterize = FALSE,
raster_dpi = 300,
cds = NULL
)Arguments
- obj
A Seurat or cell_data_set object.
- gene_or_genes
Individual gene or genes or aggregated genes to plot. Supply a character string for a single gene, a vector for multiple genes or a dataframe for aggregated genes. See description.
- assay
For Seurat objects only: the gene expression assay to get expression data from, Default: 'RNA'
- order
Whether or not to order cells by gene expression. When ordered, non-expressing cells are plotted first, i.e. on the bottom. Caution: when many cells are overplotted it may lead to a misleading presentation. Generally bb_genebubbles is a better way to present, Default: TRUE
- cell_size
Size of the points, Default: 1
- alpha
Transparency of the points, Default: 1
- ncol
Specify the number of columns if faceting, Default: NULL
- plot_title
Optional title for the plot, Default: NULL
- color_legend_title
Option to change the color scale title, Default: 'Expression'
- max_expr_val
Maximum expression value to cap the color scale, Default: NULL
- alt_dim_x
Alternate/reference dimensions to plot by.
- alt_dim_y
Alternate/reference dimensions to plot by.
- rasterize
Whether to render the graphical layer as a raster image. Default is FALSE.
- raster_dpi
If rasterize then this is the DPI used. Default = 300.
- cds
Provided for backward compatibility. If a value is supplied a warning will be emitted., Default: NULL