filterDistributions#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_giotto.R#L1418

Description#

show gene or cell distribution after filtering on expression threshold

Usage#

filterDistributions(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("raw", "normalized", "scaled", "custom"),
  expression_threshold = 1,
  detection = c("feats", "cells"),
  plot_type = c("histogram", "violin"),
  nr_bins = 30,
  fill_color = "lightblue",
  scale_axis = "identity",
  axis_offset = 0,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "filterDistributions"
)

Arguments#

Argument

Description

gobject

giotto object

feat_type

feature type

spat_unit

spatial unit

expression_values

expression values to use

expression_threshold

threshold to consider a gene expressed

detection

consider features (e.g. genes) or cells

plot_type

type of plot

nr_bins

number of bins for histogram plot

fill_color

fill color for plots

scale_axis

ggplot transformation for axis (e.g. log2)

axis_offset

offset to be used together with the scaling transformation

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_f unction <#allplotssavefunction>`__

default_save_name

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

Value#

ggplot object