Cosine cluster across hemibrain and flywire

Usage

triple_cosine_plot(
  x,
  fwtype = x,
  version = NULL,
  ...,
  threshold = 5,
  partners = c("outputs", "inputs"),
  labRow = "{type}_{abbreviate_datasets(dataset)}{side}",
  group = "type",
  heatmap = TRUE,
  interactive = FALSE,
  nas = c("zero", "drop"),
  method = c("ward.D", "single", "complete", "average", "mcquitty", "median", "centroid",
    "ward.D2")
)

Arguments

x: Hemibrain ids or a dataframe generated by triple_connection_table
fwtype: Optional flywire ids interpreted by flywire_ids function
version: Connectome data dump version. See flywire_connectome_data_version for details.
...: Additional arguments to heatmap
threshold: Minimum connection weight to be included when finding partners
partners: Whether to use output or input partners for clustering. Default now uses both.
labRow: A character vector defining labels for the rows of the resultant heatmap
group: What column to use for grouping partners.
heatmap: A logical indicating whether or not to plot the heatmap OR a function to plot the heatmap whose argument names are compatible with stats::heatmap. gplots::heatmap.2 is a good example.
interactive: When TRUE returns a shiny-based interactive heatmap
nas: What to do with rows/columns with NAs when computing cosine matrix. Dropping may be more mathematically satisfactory but eliminates neurons from the comparison, so the default is to set NA elements to do 0 similarity.
method: the clustering method. See hclust for details.

Value

A list as returned by heatmap

Details

Note that for bilateral neurons it may work better to use either input partners or output partners but not both.

Examples

# \donttest{
# AOTU063 should be separated into two subtypes.
# Very clear based on output clustering and also some small morphological differences.
triple_cosine_plot('AOTU063', partners = 'o')
#> Error in add_celltype_info(res, idcol = partner_col, version = version): Expect either character or integer64 ids!

# LAL074/LAL084 are the same type.
# Were incorrectly split due to annotation into separate hemibrain CBFs
# note that the compound type 'LAL074,LAL084' will be used to find flywire
# neurons but expanded to the regex "(LAL074|LAL084)" in order to find
# both hemibrain types
triple_cosine_plot('LAL074,LAL084', partners = 'i')
#> Matching types across datasets. Keeping 824/1276 input connections with total weight 19474/26346 (74%)

# }