plotMetaDataCellsHeatmap: plotMetaDataCellsHeatmap

View source: R/auxiliary_visuals.R

plotMetaDataCellsHeatmapR Documentation

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.