violinPlot — violinPlot • Giotto

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')

}