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Plots a biMAP scatter plot

plot_scatter_biMAP.Rd

Plots cells and genes as points. Genes are plotted on top of the cells in a larger size to make visual differentiation easier.

Usage

plot_scatter_biMAP(
  obj,
  meta_df = NULL,
  color_by = "cluster",
  cell_size = 1,
  gene_size = 2,
  cell_alpha = 0.7,
  gene_alpha = 0.8,
  color_genes = TRUE,
  label_groups = TRUE,
  group_label_size = 4,
  label_marker_genes = FALSE,
  interactive = FALSE,
  ...
)

# S4 method for caclust
plot_scatter_biMAP(
  obj,
  meta_df = NULL,
  color_by = "cluster",
  cell_size = 1,
  gene_size = 2,
  cell_alpha = 0.7,
  gene_alpha = 0.8,
  color_genes = TRUE,
  label_groups = TRUE,
  group_label_size = 4,
  label_marker_genes = FALSE,
  interactive = FALSE,
  ...
)

# S4 method for SingleCellExperiment
plot_scatter_biMAP(
  obj,
  meta_df = NULL,
  color_by = "cluster",
  cell_size = 1,
  gene_size = 2,
  cell_alpha = 0.7,
  gene_alpha = 0.8,
  color_genes = TRUE,
  label_groups = TRUE,
  group_label_size = 4,
  label_marker_genes = FALSE,
  interactive = FALSE,
  ...,
  caclust_meta_name = "caclust",
  subset = FALSE
)

plot_biMAP(
  obj,
  meta_df = NULL,
  color_by = "cluster",
  cell_size = 1,
  gene_size = 2,
  cell_alpha = 0.7,
  gene_alpha = 0.8,
  color_genes = TRUE,
  label_groups = TRUE,
  group_label_size = 4,
  label_marker_genes = FALSE,
  interactive = FALSE,
  ...
)

Arguments

obj

Object that stores biMAP coordinates. Can be either a "caclust" object or of class "SingleCellExperiment".

meta_df

optional. data.frame that should have either gene or cell names (or both) as rownames or a column named `name` and a column with the same name as `color_by`.

color_by

Either "type" or "cluster". "type" colors by the type (cell or gene) while "cluster" colors by the assigned cluster. If meta_df is provided a column from the data.frame can be specified.

cell_size

integer. Size of the cells in the plot.

gene_size

integer. Size of the genes in the plot.

cell_alpha

numeric. Alpha value of cells (between 0 and 1).

gene_alpha

numeric. Alpha value of genes (between 0 and 1).

color_genes

logical. If TRUE colors genes by color_by.

label_groups

logical. If TRUE puts the group label on the median coordinates of the point.

group_label_size

integer. Size of the group label.

label_marker_genes

logical or character vector. If TRUE, names of detected marker genes are displayed. If is character vector, the given marker genes are labeled.

interactive

If TRUE plot_scatter_biMAP returns an interactive (html) plot. If FALSE a ggplot object is returned.

...

Further arguments.

caclust_meta_name

Name under which the caclust object is stored in the metadata of the SingleCellExperiment object.

subset

Whether the biMAP embedding should be subset to the cells/genes in the SCE object. This might lead to unintended results. If unsure, we recommend to rerun CA and caclust instead.

Value

biMAP scatter plot as ggplot object.

See also

Other plot_*_biMAP: plot_contour_biMAP(), plot_hex_biMAP()