DimensionReduction: Dimension Reduction for Multi-drug Combination Visualization

In shuyuzheng/synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

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 [e-mail]

• Jing Tang [e-mail]

shuyuzheng/synergyfinder documentation built on Feb. 20, 2023, 11:33 p.m.