plotMetaDataHeatmap#

View Source Code

Last Updated: Mar 11, 2023

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.