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GenerateHeatmapInputs (similarity-based)

GenerateHeatmapInputs.Rd

Identical to GenerateHeatmapInputs_derep() but retrieves feature similarity matrices via GetSimMat() (.sim slots) and converts to distance (1 - S) when building the dist object for heatmap row clustering.

Usage

GenerateHeatmapInputs(
  mmo,
  filter_id = FALSE,
  id_list = NULL,
  filter_group = FALSE,
  group_list = NULL,
  summarize = "mean",
  control_group = "ctrl",
  normalization = "None",
  distance = NULL
)

Arguments

mmo

The mmo with sirius annotation and normalized data

filter_id

Boolean to filter features by id_list (default: FALSE)

id_list

A vector of feature names to filter (default: NULL)

filter_group

Boolean to filter groups by group_list (default: FALSE)

group_list

A vector of group names to filter (default: NULL)

summarize

The summarization method to use. Options are 'fold_change' or 'mean' (default: 'mean')

control_group

The group to use as control for fold change calculation (default: 'ctrl')

normalization

The normalization method to use. Options are 'None', 'Log', 'Meancentered', or 'Z'

distance

The distance metric to use. Options are 'dreams', 'cosine', or 'm2ds' (default: 'dreams')

Value

A list containing the following elements:

  • FC_matrix: A matrix of fold change or mean values

  • dist_matrix: A distance matrix derived from the similarity matrix as 1 - S, or NULL when distance is not supplied

  • row_label: A vector of row labels for custom-annotated features (see AddCustomAnnot()). Feature IDs are used when no custom annotation is available.

  • heatmap_data: A data frame of the heatmap values with feature IDs