A function to generate a UMAP with colors mapped to colData variables

Usage

bb_var_umap(
  obj,
  var,
  assay = "RNA",
  value_to_highlight = NULL,
  foreground_alpha = 1,
  legend_pos = "right",
  cell_size = 0.5,
  alt_stroke_color = NULL,
  legend_title = NULL,
  plot_title = NULL,
  palette = NULL,
  alt_dim_x = NULL,
  alt_dim_y = NULL,
  overwrite_labels = FALSE,
  group_label_size = 3,
  alt_label_col = NULL,
  shape = 21,
  nbin = 100,
  facet_by = NULL,
  sample_equally = FALSE,
  rasterize = FALSE,
  raster_dpi = 300,
  show_trajectory_graph = FALSE,
  trajectory_graph_color = "grey28",
  trajectory_graph_segment_size = 0.75,
  label_root_node = FALSE,
  pseudotime_dim = var,
  label_principal_points = FALSE,
  graph_label_size = 2,
  cds = NULL,
  outline_cluster = FALSE,
  outline_color = "black",
  outline_size = 1,
  outline_type = "solid",
  outline_alpha = 1,
  ...,
  man_text_df = NULL,
  text_geom = "text",
  minimum_segment_length = 1,
  hexify = FALSE,
  n_hexbins = 100
)

Arguments

obj: A Seurat or cell data set object
var: The variable to map colors to. Special exceptions are "density", "local_n" and "log_local_n" which calculate the 2 d kernel density estimate or binned cell counts and maps to color scale.
assay: The gene expression assay to draw reduced dimensions from. Default is "RNA". Does not do anything with cell_data_set objects.
value_to_highlight: Option to highlight a single value
foreground_alpha: Alpha value for foreground points
legend_pos: Legend position
cell_size: Cell point size
alt_stroke_color: Alternative color for the data point stroke
legend_title: Title for the legend
plot_title: Main title for the plot
palette: Color palette to use. "Rcolorbrewer", "Viridis" are builtin options. Otherwise provide manual values.
alt_dim_x: Alternate/reference dimensions to plot by.
alt_dim_y: Alternate/reference dimensions to plot by.
overwrite_labels: Whether to overwrite the variable value labels
group_label_size: Size of the overwritten labels
alt_label_col: Alternate column to label cells by
shape: Shape for data points
nbin: Number of bins if using var %in% c("density". "local_n", "log_local_n")
facet_by: Variable or variables to facet by.
sample_equally: Whether or not you should downsample to the same number of cells in each plot. Default is FALSE or no.
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.
show_trajectory_graph: Whether to render the principal graph for the trajectory. Requires that learn_graph() has been called on cds.
trajectory_graph_color: The color to be used for plotting the trajectory graph.
trajectory_graph_segment_size: The size of the line segments used for plotting the trajectory graph.
label_root_node: Logical; whether to label the root node for the selected pseudotime trajectory. The function will requires that a valid pseudotime column be identified, usually as the value of the "var" argument in the form of "pseudotime_cluster_value". If you wish to use var to color the cells in some other way, the pseudotime_dim argument needs to be supplied with the correct pseudotime dimension to pick the root node from.
pseudotime_dim: An alternative column to pick the pseudoetime root node from, if not supplied to var.
label_principal_points: Logical indicating whether to label roots, leaves, and branch points with principal point names. This is useful for order_cells and choose_graph_segments in non-interactive mode.
graph_label_size: How large to make the branch, root, and leaf labels.
cds: Provided for backward compatibility with prior versions. If a value is supplied, a warning will be emitted and the value will be transferred to the obj argument, Default: NULL
...: Additional params for facetting.
man_text_df: A data frame in the form of text_x = numeric_vector, text_y = numeric_vector, label = character_vector for manually placing text labels.
minimum_segment_length: Minimum length of a line to draw from label to centroid.

Value

a ggplot