get_ctd_dendro: Get CTD dendro

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Get CTD dendro

Description

Get all dendrogram features used for plotting a dendrogram of cell types.

Usage

get_ctd_dendro(ctd, annotLevel, expand = c(0, 0.66), verbose = TRUE, ...)

Arguments

ctd	Cell type data structure containing specificity_quantiles.
annotLevel	Annot level for which the gene covar file should be constructed.
expand	For position scales, a vector of range expansion constants used to add some padding around the data to ensure that they are placed some distance away from the axes. Use the convenience function expansion() to generate the values for the expand argument. The defaults are to expand the scale by 5% on each side for continuous variables, and by 0.6 units on each side for discrete variables.
verbose	Print messages.
...	Arguments passed on to prepare_quantile_groups standardise Whether to run standardise_ctd first. Provides gene ortholog conversion. input_species Which species the gene names in exp come from. See list_species for all available species. output_species Which species' genes names to convert exp to. See list_species for all available species. non121_strategy How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include: "drop_both_species" or "dbs" or 1 : Drop genes that have duplicate mappings in either the input_species or output_species (DEFAULT). "drop_input_species" or "dis" or 2 : Only drop genes that have duplicate mappings in the input_species. "drop_output_species" or "dos" or 3 : Only drop genes that have duplicate mappings in the output_species. "keep_both_species" or "kbs" or 4 : Keep all genes regardless of whether they have duplicate mappings in either species. "keep_popular" or "kp" or 5 : Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. "sum","mean","median","min" or "max" : When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species. numberOfBins Number of non-zero quantile bins.

Value

List containing ddata and ordered_cells

Source

MAGMA.Celltyping:::get_ctd_dendro(ctd = ctd, annotLevel = 1)

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.