plotHeatmap — plotHeatmap • Giotto

Creates heatmap for genes and clusters.

plotHeatmap(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes,
  cluster_column = NULL,
  cluster_order = c("size", "correlation", "custom"),
  cluster_custom_order = NULL,
  cluster_color_code = NULL,
  cluster_cor_method = "pearson",
  cluster_hclust_method = "ward.D",
  gene_order = c("correlation", "custom"),
  gene_custom_order = NULL,
  gene_cor_method = "pearson",
  gene_hclust_method = "complete",
  show_values = c("rescaled", "z-scaled", "original"),
  size_vertical_lines = 1.1,
  gradient_colors = c("blue", "yellow", "red"),
  gene_label_selection = NULL,
  axis_text_y_size = NULL,
  legend_nrows = 1,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotHeatmap"
)

Arguments

gobject: giotto object
expression_values: expression values to use
genes: genes to use
cluster_column: name of column to use for clusters
cluster_order: method to determine cluster order
cluster_custom_order: custom order for clusters
cluster_color_code: color code for clusters
cluster_cor_method: method for cluster correlation
cluster_hclust_method: method for hierarchical clustering of clusters
gene_order: method to determine gene order
gene_custom_order: custom order for genes
gene_cor_method: method for gene correlation
gene_hclust_method: method for hierarchical clustering of genes
show_values: which values to show on heatmap
size_vertical_lines: sizes for vertical lines
gradient_colors: colors for heatmap gradient
gene_label_selection: subset of genes to show on y-axis
axis_text_y_size: size for y-axis text
legend_nrows: number of rows for the cluster legend
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

Value

ggplot

Details

If you want to display many genes there are 2 ways to proceed:

1. set axis_text_y_size to a really small value and show all genes
2. provide a subset of genes to display to gene_label_selection

Examples

if (FALSE) {

data(mini_giotto_single_cell)

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

# plot heatmap
plotHeatmap(mini_giotto_single_cell,
            genes = all_genes[1:10])

# look at cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# plot heatmap per cell type, a column name from cell_metadata
plotHeatmap(mini_giotto_single_cell,
            genes = all_genes[1:10],
            cluster_column = 'cell_types')

}