Creates violinplot for selected clusters

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

if (FALSE) {

data(mini_giotto_single_cell)

# get all genes
all_genes = slot(mini_giotto_single_cell, 'gene_ID')

# look at cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# plot violinplot with selected genes and stratified for identified cell types
violinPlot(mini_giotto_single_cell,
           genes = all_genes[1:10],
           cluster_column = 'cell_types')

}