violinPlot

violinPlot

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

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

feats

features to plot

genes

deprecated, use feats argument

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