violinPlot: violinPlot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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

Value

ggplot

Examples

## Not run: 

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')


## End(Not run)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.