plotMetaDataHeatmap#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/auxiliary_visuals.R#L1222

Description#

Creates heatmap for genes within aggregated clusters.

Usage#

plotMetaDataHeatmap(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  metadata_cols = NULL,
  selected_feats = NULL,
  selected_genes = NULL,
  first_meta_col = NULL,
  second_meta_col = NULL,
  show_values = c("zscores", "original", "zscores_rescaled"),
  custom_cluster_order = NULL,
  clus_cor_method = "pearson",
  clus_cluster_method = "complete",
  custom_feat_order = NULL,
  custom_gene_order = NULL,
  feat_cor_method = "pearson",
  gene_cor_method = NULL,
  feat_cluster_method = "complete",
  gene_cluster_method = NULL,
  gradient_color = c("blue", "white", "red"),
  gradient_midpoint = 0,
  gradient_limits = NULL,
  x_text_size = 10,
  x_text_angle = 45,
  y_text_size = 10,
  strip_text_size = 8,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotMetaDataHeatmap"
)

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?)

metadata_cols

annotation columns found in pDataDT(gobject)

selected_feats

subset of features to use

selected_genes

deprecated. See selected_feats param

first_meta_col

if more than 1 metadata column, select the x-axis factor

second_meta_col

if more than 1 metadata column, select the facetting factor

show_values

which values to show on heatmap (e.g. “zscores?, “original?, “zscores_rescaled?)

custom_cluster_order

custom cluster order (default = NULL)

clus_cor_method

correlation method for clusters, default to “pearson?

clus_cluster_method

hierarchical cluster method for the clusters, default to “complete?

custom_feat_order

custom feature order (default = NULL)

custom_gene_order

deprecated. See custom_feat_order param

feat_cor_method

correlation method for features, default to “pearson?

gene_cor_method

deprecated. See feat_cor_method param

feat_cluster_method

hierarchical cluster method for the features, default to “complete?

gene_cluster_method

deprecated. See feat_cluster_method param

gradient_color

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

x_text_size

size of x-axis text

x_text_angle

angle of x-axis text

y_text_size

size of y-axis text

strip_text_size

size of strip text

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#

Creates heatmap for the average expression of selected genes in the different annotation/cluster groups. Calculation of cluster or gene order is done on the provided expression values, but visualization is by default on the z-scores. Other options are the original values or z-scores rescaled per gene (-1 to 1).

Value#

ggplot or data.table

Seealso#

`plotMetaDataCellsHeatmap <#plotmetadatacellsheatmap>`__ for numeric cell annotation instead of gene expression.