Plot Heatmap

plotHeatmap()

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

A ggplot value.

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')

}