dot-ExtractMultiDrugPlotData: Extract Data Table and Annotation Information for Multi-drug...

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

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 [e-mail]

• Jing Tang [e-mail]

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