filterDistributions

show gene or cell distribution after filtering on expression threshold

filterDistributions(
  gobject,
  expression_values = c("raw", "normalized", "scaled", "custom"),
  expression_threshold = 1,
  detection = c("genes", "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

gobject

giotto object

expression_values

expression values to use

expression_threshold

threshold to consider a gene expressed

detection

consider 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_function

default_save_name

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

Value

ggplot object

Examples

data(mini_giotto_single_cell)

# distribution plot of genes
filterDistributions(mini_giotto_single_cell, detection = 'genes')

# distribution plot of cells
filterDistributions(mini_giotto_single_cell, detection = 'cells')