Skip to contents

Wrapper function for Bonsai parameters

params_sc_bonsai.Rd

Parameters for bonsai_sc(). Sanity turns the raw counts into posterior log fold changes with error bars, Bonsai builds a tree over the cells from those, and the tree is laid out in 2D for plotting. The Sanity defaults come from sanity-sc-rs, the search defaults from bonsai-rs.

Usage

params_sc_bonsai(
  variance_rule = c("marginalise", "posterior_mean", "max_posterior", "fixed"),
  fixed_variance = NULL,
  variance_bins = 161L,
  variance_min = 0.001,
  variance_max = 50,
  min_signal_to_noise = 1,
  start = c("linkage", "greedy_merge"),
  spr_search = c("approximate", "exact"),
  nni_search = c("approximate", "exact"),
  seed = 42L,
  reroot = TRUE,
  layout = c("equal_angle", "equal_daylight", "dendrogram"),
  hyperbolic = FALSE
)

Arguments

variance_rule

String. How Sanity treats each gene's variance in log fold change. "marginalise" integrates over the variance grid, "posterior_mean" and "max_posterior" collapse it to one value first (cheaper, less accurate error bars), and "fixed" uses fixed_variance for every gene. One of c("marginalise", "posterior_mean", "max_posterior", "fixed"). Defaults to "marginalise".

fixed_variance

Numeric or NULL. The variance for variance_rule = "fixed". Ignored otherwise. Defaults to NULL.

variance_bins

Integer. Bins in the log-spaced variance grid. Defaults to 161L.

variance_min

Numeric. Smallest variance on the grid. Defaults to 0.001.

variance_max

Numeric. Largest variance on the grid. Defaults to 50.0.

min_signal_to_noise

Numeric. Genes whose signal-to-noise ratio falls below this are left out of the tree. Defaults to 1.0.

start

String. Initial topology. "linkage" is a Ward linkage over a neighbour graph: faster and a better tree on real data. "greedy_merge" is the paper's star merge, kept for comparisons with the published method. One of c("linkage", "greedy_merge"). Defaults to "linkage".

String. Subtree pruning and regrafting. "approximate" stays within a few nats of "exact" on bonsai-rs's benchmarks at up to twice the speed. One of c("approximate", "exact"). Defaults to "approximate".

String. Nearest-neighbour interchange. "approximate" found the same tree as "exact" on every bonsai-rs benchmark, and faster. One of c("approximate", "exact"). Defaults to "approximate".

seed

Integer. Seed for the linkage, SPR and NNI searches. Defaults to 42L.

reroot

Boolean. Reroot the finished tree for display. Changes the drawing, not the likelihood. Defaults to TRUE.

layout

String. 2D layout. "equal_daylight" refines equal angle but falls back to it above 2,048 nodes, so it only matters for small trees. Can be changed later with relayout_bonsai(). One of c("equal_angle", "equal_daylight", "dendrogram"). Defaults to "equal_angle".

hyperbolic

Boolean. Project the layout onto the hyperbolic disk. Defaults to FALSE.

Value

A named list with the following elements:

  • variance_rule - String. How Sanity treats each gene's variance in log fold change. "marginalise" integrates over the variance grid, "posterior_mean" and "max_posterior" collapse it to one value first (cheaper, less accurate error bars), and "fixed" uses fixed_variance for every gene. One of c("marginalise", "posterior_mean", "max_posterior", "fixed"). Defaults to "marginalise".

  • fixed_variance - Numeric or NULL. The variance for variance_rule = "fixed". Ignored otherwise. Defaults to NULL.

  • variance_bins - Integer. Bins in the log-spaced variance grid. Defaults to 161L.

  • variance_min - Numeric. Smallest variance on the grid. Defaults to 0.001.

  • variance_max - Numeric. Largest variance on the grid. Defaults to 50.0.

  • min_signal_to_noise - Numeric. Genes whose signal-to-noise ratio falls below this are left out of the tree. Defaults to 1.0.

  • start - String. Initial topology. "linkage" is a Ward linkage over a neighbour graph: faster and a better tree on real data. "greedy_merge" is the paper's star merge, kept for comparisons with the published method. One of c("linkage", "greedy_merge"). Defaults to "linkage".

  • spr_search - String. Subtree pruning and regrafting. "approximate" stays within a few nats of "exact" on bonsai-rs's benchmarks at up to twice the speed. One of c("approximate", "exact"). Defaults to "approximate".

  • nni_search - String. Nearest-neighbour interchange. "approximate" found the same tree as "exact" on every bonsai-rs benchmark, and faster. One of c("approximate", "exact"). Defaults to "approximate".

  • seed - Integer. Seed for the linkage, SPR and NNI searches. Defaults to 42L.

  • reroot - Boolean. Reroot the finished tree for display. Changes the drawing, not the likelihood. Defaults to TRUE.

  • layout - String. 2D layout. "equal_daylight" refines equal angle but falls back to it above 2,048 nodes, so it only matters for small trees. Can be changed later with relayout_bonsai(). One of c("equal_angle", "equal_daylight", "dendrogram"). Defaults to "equal_angle".

  • hyperbolic - Boolean. Project the layout onto the hyperbolic disk. Defaults to FALSE.

References

de Groot, et al., Nat. Biotechnol., 2026; Breda, et al., Nat. Biotechnol., 2021.