violinPlot#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_visuals.R#L1721

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 (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 `showSaveP arameters <#showsaveparameters>`__

default_save_name

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

Value#

ggplot