plotMetaDataCellsHeatmap: plotMetaDataCellsHeatmap

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plotMetaDataCellsHeatmap

Description

Creates heatmap for numeric cell metadata within aggregated clusters.

Usage

plotMetaDataCellsHeatmap(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  metadata_cols = NULL,
  spat_enr_names = NULL,
  value_cols = 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_values_order = NULL,
  values_cor_method = "pearson",
  values_cluster_method = "complete",
  midpoint = 0,
  x_text_size = 8,
  x_text_angle = 45,
  y_text_size = 8,
  strip_text_size = 8,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotMetaDataCellsHeatmap"
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
metadata_cols	annotation columns found in pDataDT(gobject)
spat_enr_names	spatial enrichment results to include
value_cols	value columns to use
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_values_order	custom values order (default = NULL)
values_cor_method	correlation method for values, default to "pearson"
values_cluster_method	hierarchical cluster method for the values, default to "complete"
midpoint	midpoint of show_values
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 for saving, don't change, change save_name in save_param

Details

Creates heatmap for the average values of selected value columns in the different annotation groups.

Value

ggplot or data.table

See Also

plotMetaDataHeatmap for gene expression instead of numeric cell annotation data.

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