plotHeatmap#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_visuals.R#L958

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 (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 `showSaveP arameters <#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