DimensionReduction {synergyfinder} | R Documentation

## Dimension Reduction for Multi-drug Combination Visualization

### Description

This function will take the multi-drug combination data, project the concentrations of all the drugs into 2 dimensions. It is an auxiliary function for PlotMultiDrugSurface

### Usage

    DimensionReduction(
      plot_table,
      drug_pair,
      plot_value,
      distance_method = "mahalanobis"
    )

### Arguments

`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_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.
`distance_method` | The methods to calculate the distance between different data points from the concentration of drugs. The distance matrix is used for dimension reduction. This parameter is used to set the parameter `method` for vegdist. The default values is "mahalanobis".

### Value

A data frame. It contains the plot information required by function GenerateSurface

### Author(s)

- Shuyu Zheng shuyu.zheng@helsinki.fi

- Jing Tang jing.tang@helsinki.fi

[Package synergyfinder version 3.0.14 Index]