filterCombinations

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

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),
  min_det_feats_per_cell = c(200, 400),
  scale_x_axis = "identity",
  x_axis_offset = 0,
  scale_y_axis = "identity",
  y_axis_offset = 0,
  show_plot = TRUE,
  return_plot = FALSE,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "filterCombinations"
)

Arguments

gobject

giotto object

feat_type

feature type (e.g. "rna", "dna", "protein")

spat_unit

spatial unit (e.g. "cell")

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

min_det_feats_per_cell

minimum # of features that need to be detected in a 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

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

Value

list of data.table and ggplot object

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.

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

filterCombinations(g)