biMAP plotter — biMAP_plotter • CAbiNet

This function plots the different variants of biMAP

Usage

biMAP_plotter(
  caclust,
  color_by = "cluster",
  meta_df = NULL,
  type = "scatter",
  cell_size = 1,
  gene_size = 3,
  cell_alpha = 0.5,
  gene_alpha = 1,
  hex_n = 40,
  min_bin = 2,
  show_density = FALSE,
  contour_n = 5,
  color_genes = TRUE,
  label_groups = TRUE,
  group_label_size = 4,
  label_marker_genes = FALSE,
  colors = NULL,
  plotly = FALSE,
  max.overlaps = 12
)

Arguments

caclust: caclust object with biMAP stored.
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.
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`.
type: Determines the kind of plot outputted. Either "scatter" (scatter plot), "contour" (density contour plot) or "hex" (binned hexagonals).
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).
hex_n: integer. Number of hexagonal bins that partition the x-axis.
min_bin: integer. Only bins with more than `min_bin` cells are plotted.
show_density: logical. Should the alpha value for plot type "hex" be adjusted by the number of cells in the bin?
contour_n: integer. Number of contour lines to plot.
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.
colors: Vector of hexadecimal color codes of the same length as the categories defined by color_by or longer. If NULL ignored.
plotly: If TRUE a hex plot with labels per hexbin will be made.
max.overlaps: Exclude text labels that overlap too many things.

Value

biMAP plot as ggplot object.