Dimension plot with background
plot_split_dimred.RdThis function is an equivalent of Seurat::DimPlot, adapted to a split.by representation with gray background.
Usage
plot_split_dimred(
sobj = sobj,
reduction = "umap",
split_by = "orig.ident",
group_by = NULL,
color_by = NULL,
bg_pt_size = 0.25,
main_pt_size = 0.25,
split_color = NULL,
group_color = NULL,
color_palette = NULL,
bg_color = "gray92",
order = FALSE
)Arguments
- sobj
A Seurat object (no default)
- reduction
CHARACTER : name of a reduction present in the Seurat object (default to 'umap')
- split_by
CHARACTER : name of a column in metadata, to split the representation by (default to 'orig.ident')
- group_by
CHARACTER : name of a column in metadata, to group the color on split representation (default to NULL)
- color_by
CHARACTER : name that can be retrieve using Seurat::FetchData, to color cells by on representation (default to NULL)
- bg_pt_size
FLOAT : point size for the gray background (default to 0.25)
- main_pt_size
FLOAT : point size for the cells (default to 0.25)
- split_color
CHARACTER : named vector of colors for the levels of split_by, to color subplot titles (default to black)
- group_color
CHARACTER : named vector of colors for the levels of group_color, to color cells in subplots (default to ggplot default colors)
- color_palette
CHARACTER : a vector of colors to plot cells by color_by (default to aquarius::palette_GrOrBl palette)
- bg_color
CHARACTER : the color for the gray background (default to 'gray92')
- order
LOGICAL : whether to order cells by levels (group_by : first level on top) or by intensities (color_by : higher values on top), or not (default to FALSE)