plotHeatmap

plotHeatmap

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

Argument	Description
gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
expression_values	expression values to use
feats	features to use
genes	deprecated, use feats
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
feat_order	method to determine features order
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
gene_cor_method	deprecated, use feat_cor_method
feat_hclust_method	method for hierarchical clustering of features
gene_hclust_method	deprecated, use feat_hclust_method
show_values	which values to show on heatmap
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
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see ``showSaveParameters` <#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