filterCombinations#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_giotto.R#L1601

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#

Argument

Description

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_f unction <#allplotssavefunction>`__

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