filterCombinations

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Last Updated: Mar 11, 2023

Description

Shows how many genes and cells are lost with combinations of thresholds.

Usage

filterCombinations(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("raw", "normalized", "scaled", "custom"),
  expression_thresholds = c(1, 2),
  feat_det_in_min_cells = c(5, 50),
  gene_det_in_min_cells = NULL,
  min_det_feats_per_cell = c(200, 400),
  min_det_genes_per_cell = NULL,
  scale_x_axis = "identity",
  x_axis_offset = 0,
  scale_y_axis = "identity",
  y_axis_offset = 0,
  show_plot = TRUE,
  return_plot = FALSE,
  save_plot = NA,
  save_param = list(),
  default_save_name = "filterCombinations"
)

Arguments

gobject	giotto object
feat_type	feature type
spat_unit	spatial unit
expression_values	expression values to use
expression_thresholds	all thresholds to consider a gene expressed
feat_det_in_min_cells	minimum # of cells that need to express a feature
gene_det_in_min_cells	deprecated, use feat_det_in_min_cells
min_det_feats_per_cell	minimum # of features that need to be detected in a cell
min_det_genes_per_cell	deprecated, use min_det_feats_per_cell
scale_x_axis	ggplot transformation for x-axis (e.g. log2)
x_axis_offset	x-axis offset to be used together with the scaling transformation
scale_y_axis	ggplot transformation for y-axis (e.g. log2)
y_axis_offset	y-axis offset to be used together with the scaling transformation
show_plot	show plot
return_plot	return only ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters from all_plots_save_function
default_save_name	default save name for saving, don’t change, change save_name in save_param

Details

Creates a scatterplot that visualizes the number of genes and cells that are lost with a specific combination of a gene and cell threshold given an arbitrary cutoff to call a gene expressed. This function can be used to make an informed decision at the filtering step with filterGiotto.

Value

list of data.table and ggplot object