Make Clustering Report

Generates a detailed clustering report including heatmaps, dendrograms, curve plots, and consensus shapes for each level within a condition.

Usage

make_clustering_report(
  all_levels_clustering,
  condition,
  data,
  meta,
  annotation,
  genes,
  spline_params,
  adj_pthresholds,
  adj_pthresh_avrg_diff_conditions,
  adj_pthresh_interaction_condition_time,
  report_dir,
  mode,
  report_info,
  design,
  meta_batch_column,
  meta_batch2_column,
  plot_info,
  plot_options,
  feature_name_columns,
  spline_comp_plots
)

Arguments

all_levels_clustering: A list containing clustering results for each level within a condition.
condition: A character string specifying the condition.
data: A matrix of data values.
meta: A dataframe containing metadata.
annotation: Dataframe containig the annotation info of the features, such as gene and uniprotID, for example.
genes: Character vector containing the genes of the features.
spline_params: A list of spline parameters for the analysis.
adj_pthresholds: Numeric vector, containing a float < 1 > 0 as each value. There is one float for every level, and this is the adj. p-value threshold.
adj_pthresh_avrg_diff_conditions: Float
adj_pthresh_interaction_condition_time: Float
report_dir: A character string specifying the report directory.
mode: A character string specifying the mode ('isolated' or 'integrated').
report_info: An object containing report information.
design: A string representing the limma design formula
meta_batch_column: A character string specifying the meta batch column.
meta_batch2_column: A character string specifying the second meta batch column.
plot_info: List containing the elements y_axis_label (string), time_unit (string), treatment_labels (character vector), treatment_timepoints (integer vector). All can also be NA. This list is used to add this info to the spline plots. time_unit is used to label the x-axis, and treatment_labels and -timepoints are used to create vertical dashed lines, indicating the positions of the treatments (such as feeding, temperature shift, etc.).
plot_options: List with specific fields (cluster_heatmap_columns = Bool) that allow for customization of plotting behavior.
feature_name_columns: Character vector containing the column names of the annotation info that describe the features. This argument is used to specify in the HTML report how exactly the feature names displayed above each individual spline plot have been created. Use the same vector that was used to create the row headers for the data matrix!
spline_comp_plots: List containing the list of lists with all the plots for all the pairwise comparisons of the condition in terms of average spline diff and interaction condition time, and another list of lists where the respective names of each plot are stored.

Value

No return value, called for side effects.

Usage

Arguments

Value

See also