plotMetaDataCellsHeatmap

plotMetaDataCellsHeatmap

Description

Creates heatmap for numeric cell metadata within aggregated clusters.

Usage

plotMetaDataCellsHeatmap(
  gobject,
  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

Argument	Description
gobject	giotto object
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
custom_cluster_order	custom cluster order (default = NULL)
clus_cor_method	correlation method for clusters
clus_cluster_method	hierarchical cluster method for the clusters
custom_values_order	custom values order (default = NULL)
values_cor_method	correlation method for values
values_cluster_method	hierarchical cluster method for the values
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
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see ``showSaveParameters` <#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

Seealso

``plotMetaDataHeatmap` <#plotmetadataheatmap>`_ for gene expression instead of numeric cell annotation data.