violinPlot#

Last Updated: Nov 17, 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