violinPlot

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Last Updated: Mar 11, 2023

Description

Creates violinplot for selected clusters

Usage

violinPlot(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats = NULL,
  genes = NULL,
  cluster_column,
  cluster_custom_order = NULL,
  color_violin = c("feats", "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
spat_unit	spatial unit (e.g. “cell”)
feat_type	feature type (e.g. “rna”, “dna”, “protein”)
expression_values	expression values to use (e.g. “normalized”, “scaled”, “custom”)
feats	features to plot
genes	deprecated, use feats argument
cluster_column	name of column to use for clusters (e.g. “leiden_clus”)
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 (e.g. “top”, “right”, “left”, “bottom”)
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. TRUE or FALSE
return_plot	return ggplot object. TRUE or FALSE
save_plot	directly save the plot. TRUE or FALSE
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