.ExtractMultiDrugPlotData {synergyfinder} | R Documentation

## Extract Data Table and Annotation Information for Multi-drug Plotting

### Description

This function extracts the information for Multi-drug plotting from input list `data`. It is an auxiliary function for PlotMultiDrugSurface and PlotMultiDrugBar.

### Usage

    .ExtractMultiDrugPlotData(
      data,
      plot_block = 1,
      plot_value = "response",
      summary_statistic = NULL,
      statistic = NULL,
      titles = TRUE
    )

### Arguments

`data` | A list object generated by function `ReshapeData`.
`plot_block` | A character/integer. It indicates the block ID for the block to visualize.
`plot_value` | A vector of characters. It contains the name of one or more metrics to be visualized. If the `data` is the direct output from ReshapeData, the values for this parameter are: response_origin The original response value in input data. It might be % inhibition or % viability. response The % inhibition after preprocess by function ReshapeData If the `data` is the output from CalculateSynergy, following values are also available: ZIP_ref, Bliss_ref, HSA_ref, Loewe_ref The reference additive effects calculated by ZIP, Bliss, HSA or Loewe model, respectively. ZIP_synergy, Bliss_synergy, HSA_synergy, Loewe_synergy The synergy score calculated by ZIP, Bliss, HSA or Loewe model, respectively. ZIP_fit The response fitted by ZIP model.
`summary_statistic` | A vector of characters or NULL. It indicates the summary statistics for all the `plot_value` in whole combination matrix. Available values are: mean Median value for all the responses or synergy scores in the matrix and the p-value if it is valid; median Median value for all the responses or synergy scores in the matrix; quantile_90 90% quantile. User could change the number to print different sample quantile. For example quantile_50 equal to median. If it is `NULL`, no statistics will be printed.
`statistic` | A character or NULL. It indicates the statistics printed in the plot while there are replicates in input data. Available values are: sem Standard error of mean; ci 95 If it is `NULL`, no statistics will be printed.
`titles` | A logical value. If it is `TRUE`, the plot tile, subtilte, and title for z axis will be extracted and output.

### Value

A list. It contains the elements:

- plot_table A data frame contains concentrations for all drugs, the values for `plot_value`.

- drug_pair A data frame contains the drug names and concentration unites, whither the block is replicate or not.

- plot_subtitle A string for plot subtitle.

- plot_title A string for plot title.

- z_axis_subtitle A string for plot z-axis title.

### Author(s)

- Shuyu Zheng shuyu.zheng@helsinki.fi

- Jing Tang jing.tang@helsinki.fi

[Package synergyfinder version 3.0.14 Index]