bb_gene_umap: Make a Plot of Gene Expression in UMAP Form

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

Make a Plot of Gene Expression in UMAP Form

Description

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

Value

A ggplot

See Also

normalized_counts as_tibble pivot_longer mutate-joins, mutate, select, arrange ggplot, aes, geom_point, scale_colour_viridis_d, labs, facet_wrap, vars, theme, margin

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.