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" )
| 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 |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
ggplot
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') }