`calculateHVG`¶

calculateHVG

Description¶

compute highly variable genes

Usage¶

calculateHVG(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  method = c("cov_groups", "cov_loess"),
  reverse_log_scale = FALSE,
  logbase = 2,
  expression_threshold = 0,
  nr_expression_groups = 20,
  zscore_threshold = 1.5,
  HVGname = "hvg",
  difference_in_cov = 0.1,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "HVGplot",
  return_gobject = TRUE
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	expression values to use
`method`	method to calculate highly variable genes
`reverse_log_scale`	reverse log-scale of expression values (default = FALSE)
`logbase`	if reverse_log_scale is TRUE, which log base was used?
`expression_threshold`	expression threshold to consider a gene detected
`nr_expression_groups`	number of expression groups for cov_groups
`zscore_threshold`	zscore to select hvg for cov_groups
`HVGname`	name for highly variable genes in cell metadata
`difference_in_cov`	minimum difference in coefficient of variance required
`show_plot`	show plot
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters from ``all_plots_save_function` <#allplotssavefunction>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param
`return_gobject`	boolean: return giotto object (default = TRUE)

Details¶

Currently we provide 2 ways to calculate highly variable genes:

list(“1. high coeff of variance (COV) within groups: “) list() First genes are binned ( list(“nr_expression_groups”) ) into average expression groups and the COV for each gene is converted into a z-score within each bin. Genes with a z-score higher than the threshold ( list(“zscore_threshold”) ) are considered highly variable. list()

list(“2. high COV based on loess regression prediction: “) list() A predicted COV is calculated for each gene using loess regression (COV~log(mean expression)) Genes that show a higher than predicted COV ( list(“difference_in_cov”) ) are considered highly variable. list()

Value¶

giotto object highly variable genes appended to gene metadata (fDataDT)

Examples¶

data(mini_giotto_single_cell) # loads existing Giotto object

# update a giotto object
mini_giotto_single_cell <- calculateHVG(gobject = mini_giotto_single_cell,
zscore_threshold = 0.1,
nr_expression_groups = 3)

# return a data.table with the high variable genes annotated
hvg_dt <- calculateHVG(gobject = mini_giotto_single_cell,
zscore_threshold = 0.1, nr_expression_groups = 3,
return_plot = FALSE, return_gobject = FALSE)

# return the ggplot object
hvg_plot <- calculateHVG(gobject = mini_giotto_single_cell,
zscore_threshold = 0.1, nr_expression_groups = 3,
return_plot = TRUE, return_gobject = FALSE)