plotMetaDataHeatmap: plotMetaDataHeatmap

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotMetaDataHeatmap

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

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 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

See Also

plotMetaDataCellsHeatmap for numeric cell annotation instead of gene expression.

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.