plotMetaDataCellsHeatmap#

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Last Updated: Mar 11, 2023

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.