filterDistributions: filterDistributions

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

show gene or cell distribution after filtering on expression threshold

Usage

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')

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.