violinPlot: violinPlot

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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

    violinPlot(gobject)

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