Show Gene Distributions

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

A 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')