`violinPlot`¶

violinPlot

Description¶

Creates violinplot for selected clusters

Usage¶

violinPlot(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes,
  cluster_column,
  cluster_custom_order = NULL,
  color_violin = c("genes", "cluster"),
  cluster_color_code = NULL,
  strip_position = c("top", "right", "left", "bottom"),
  strip_text = 7,
  axis_text_x_size = 10,
  axis_text_y_size = 6,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "violinPlot"
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	expression values to use
`genes`	genes to plot
`cluster_column`	name of column to use for clusters
`cluster_custom_order`	custom order of clusters
`color_violin`	color violin according to genes or clusters
`cluster_color_code`	color code for clusters
`strip_position`	position of gene labels
`strip_text`	size of strip text
`axis_text_x_size`	size of x-axis text
`axis_text_y_size`	size of y-axis text
`show_plot`	show plot
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Value¶

ggplot

Examples¶

data(mini_giotto_single_cell)

# get all genes
all_genes = slot(mini_giotto_single_cell, 'gene_ID')

# look at cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# plot violinplot with selected genes and stratified for identified cell types
violinPlot(mini_giotto_single_cell,
genes = all_genes[1:10],
cluster_column = 'cell_types')