plotMetaDataCellsHeatmap: plotMetaDataCellsHeatmap

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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

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
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.

Examples

    plotMetaDataCellsHeatmap(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.