plotHeatmap#

Last Updated: Mar 11, 2023

Description#

Creates heatmap for genes and clusters.

Usage#

plotHeatmap(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats,
  genes = NULL,
  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",
  feat_order = c("correlation", "custom"),
  gene_order = NULL,
  feat_custom_order = NULL,
  gene_custom_order = NULL,
  feat_cor_method = "pearson",
  gene_cor_method = NULL,
  feat_hclust_method = "complete",
  gene_hclust_method = NULL,
  show_values = c("rescaled", "z-scaled", "original"),
  size_vertical_lines = 1.1,
  gradient_colors = c("blue", "yellow", "red"),
  feat_label_selection = NULL,
  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
`spat_unit`	spatial unit (e.g. “cell”)
`feat_type`	feature type (e.g. “rna”, “dna”, “protein”)
`expression_values`	expression values to use (e.g. “normalized”, “scaled”, “custom”)
`feats`	features to use
`genes`	deprecated, use feats
`cluster_column`	name of column to use for clusters (e.g. “leiden_clus”)
`cluster_order`	method to determine cluster order (e.g. “size”, “correlation”, “custom”)
`cluster_custom_order`	custom order for clusters
`cluster_color_code`	color code for clusters
`cluster_cor_method`	method for cluster correlation, default to “pearson”
`cluster_hclust_method`	method for hierarchical clustering of clusters, default to “ward.D”
`feat_order`	method to determine features order (e.g. “correlation”, “custom”)
`gene_order`	deprecated, use feat_order
`feat_custom_order`	custom order for features
`gene_custom_order`	deprecated, use feat_custom_order
`feat_cor_method`	method for features correlation, default to “pearson”
`gene_cor_method`	deprecated, use feat_cor_method
`feat_hclust_method`	method for hierarchical clustering of features, default to “complete”
`gene_hclust_method`	deprecated, use feat_hclust_method
`show_values`	which values to show on heatmap (e.g. “rescaled”, “z-scaled”, “original”)
`size_vertical_lines`	sizes for vertical lines
`gradient_colors`	colors for heatmap gradient
`feat_label_selection`	subset of features to show on y-axis
`gene_label_selection`	deprecated, use feat_label_selection
`axis_text_y_size`	size for y-axis text
`legend_nrows`	number of rows for the cluster legend
`show_plot`	show plot. TRUE or FALSE
`return_plot`	return ggplot object. TRUE or FALSE
`save_plot`	directly save the plot. TRUE or FALSE
`save_param`	list of saving parameters, see `showSaveParameters`
`default_save_name`	default save name

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 features
1. provide a subset of features to display to feat_label_selection

Value#

ggplot