plot_dimred: Plot dimensional reduction from SCE

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

Plot dimensional reduction from SCE

Description

Plot dimensional reduction from SCE

Usage

plot_dimred(
  object,
  colour_by,
  colour_list_in_metadata = "colors",
  colours_reduce_labels = TRUE,
  features_add = c(),
  dimred = "UMAP",
  columns = NULL,
  by_exprs_values = "logcounts",
  seed = 12232,
  order = FALSE,
  order_function = function(x) {
     order(x, decreasing = FALSE, na.last = FALSE)
 },
  shuffle = FALSE,
  point_size = 0.5,
  point_alpha = 1,
  max.cutoff = NA,
  min.cutoff = NA,
  scale_color = NULL,
  value_convert = NULL,
  text_by = NULL,
  text_by_colour = "black",
  text_by_dimred_summary_fun = median,
  text_by_size = NA,
  text_by_fontface = "bold",
  text_by_padding = unit(0.01, units = "npc"),
  text_by_fill = alpha(c("white"), 0.75),
  text_repel = TRUE,
  text_repel_max_overlaps = Inf,
  coldata_exclude_class = c("CompressedSplitDFrameList"),
  rasterise = FALSE,
  rasterise_dev = "cairo",
  rasterise_dpi = 300,
  rasterise_scale = 1,
  ...
)

Arguments

object	SingleCellExperiment object
colour_by	Variable to use for coloring
colour_list_in_metadata	If set, function will search for a manual colouring vector in the metadata(sce)[[colour_list_in_metadata]][[colour_by]]
colours_reduce_labels	If TRUE, reduce colour legend to only show values included in the plot
features_add	Fetch additional features to data.frame given to ggplot (for specialized plotting)
dimred	Which dimensional reductions should be used?
columns	Vector of columns in SCE to plot
by_exprs_values	SCE Assay to use
seed	Seed for random operations
order	Should points plotted in order by their value
order_function	What function should be used for ordering?
shuffle	Should points be plotted in random order
point_size	Size of individual points
point_alpha	Alpha level of each point
max.cutoff	Cutoff value for upper limit (can be integer or 'q' value for quantile: 'q95' sets at 95% percentile)
min.cutoff	Cutoff value for lower limit (see max.cutoff)
scale_color	Color scale to use (viridis by default)
value_convert	Function to convert values before plotting (If NULL, no conversion)
text_by	Variable to use for labelling
text_by_colour	Label color if text_by is set (black by default)
text_by_dimred_summary_fun	Which function should be used to place text_by (default median)
text_by_size	Text size if text_by is set
text_by_fontface	Fontface is text_by is set (default "bold")
text_by_padding	Label padding if text_by is set.
text_by_fill	Label fill if text_by is set (alpha("white", 0.75) default)
text_repel	Should text labels be repelled from each other?
text_repel_max_overlaps	Max overlaps for ggrepel
coldata_exclude_class	By default loads all colData except the columns of the classes included in this vector
rasterise	Should points be rasterised (ggrastr)?
rasterise_dev	What device should be used for rasterisation?
rasterise_dpi	What DPI should be used for rasterisation?
rasterise_scale	What scale should be used for rasterisation?
...	Passed on to makePerCellDF

Value

ggplot2 object

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.