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Calculate Highly Variable Features for GiottoDB

Source: R/calculateHVF_S3.R
calculateHVF.Rd

S3 method that prevents accessing "scaled" expression to avoid materialization.

Usage

calculateHVF(gobject, ...)

# S3 method for class 'GiottoDB'
calculateHVF(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = "normalized",
  method = c("cov_groups", "cov_loess", "var_p_resid"),
  reverse_log_scale = FALSE,
  logbase = 2,
  expression_threshold = 0,
  nr_expression_groups = 20,
  zscore_threshold = 1.5,
  HVFname = "hvf",
  difference_in_cov = 0.1,
  var_threshold = 1.5,
  var_number = NULL,
  random_subset = NULL,
  set_seed = TRUE,
  seed_number = 1234,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "HVFplot",
  return_gobject = TRUE,
  calc_gini = TRUE,
  verbose = TRUE
)

# S3 method for class 'giotto'
calculateHVF(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  method = c("cov_groups", "cov_loess", "var_p_resid"),
  reverse_log_scale = FALSE,
  logbase = 2,
  expression_threshold = 0,
  nr_expression_groups = 20,
  zscore_threshold = 1.5,
  HVFname = "hvf",
  difference_in_cov = 0.1,
  var_threshold = 1.5,
  var_number = NULL,
  random_subset = NULL,
  set_seed = TRUE,
  seed_number = 1234,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "HVFplot",
  return_gobject = TRUE,
  calc_gini = TRUE,
  verbose = TRUE
)

Arguments

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

method

method to calculate highly variable features

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

(cov_groups) number of expression groups for cov_groups

zscore_threshold

(cov_groups) zscore to select hvg for cov_groups

HVFname

name for highly variable features in cell metadata

difference_in_cov

(cov_loess) minimum difference in coefficient of variance required

var_threshold

(var_p_resid) variance threshold for features for var_p_resid method

var_number

(var_p_resid) number of top variance features for var_p_resid method

random_subset

random subset to perform HVF detection on. Passing NULL runs HVF on all cells.

set_seed

logical. whether to set a seed when random_subset is used

seed_number

seed number to use when random_subset is used

show_plot

show plot

return_plot

return ggplot object (overridden by return_gobject)

save_plot

logical. directly save the plot

save_param

list of saving parameters from GiottoVisuals::all_plots_save_function()

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)

calc_gini

logical. Whether to calculate Gini index for each feature. Set to FALSE for performance with large datasets or dbMatrix objects.

verbose

be verbose