Plot2DrugSurface {synergyfinder} | R Documentation

## 3D Surface Plot for 2-drug Combination Dose-Response/Synergy Scores

### Description

This function will generate a surface plot for 2-drug combinations. The axes are the dosage for each drug. The values could be observed response, synergy scores or the reference effects calculated from different models.

### Usage

    Plot2DrugSurface(
      data,
      plot_block = 1,
      drugs = c(1, 2),
      plot_value = "response",
      summary_statistic = NULL,
      plot_title = NULL,
      interpolate_len = 2,
      col_range = NULL,
      row_range = NULL,
      dynamic = FALSE,
      grid = TRUE,
      high_value_color = "#FF0000",
      low_value_color = "#00FF00",
      text_size_scale = 1
    )

### Arguments

`data` | A list object generated by function `ReshapeData`.
`plot_block` | A character/integer. It indicates the block ID for the block to visualize.
`drugs` | A vector of characters or integers with length of 2. It contains the index for two drugs to plot. For example, `c(1, 2)` indicates to plot "drug1" and "drug2" in the input `data`.
`plot_value` | A character value. It indicates the score or response value to be visualized. If the `data` is the direct output from ReshapeData, the available 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.
`plot_title` | A character value. It specifies the plot title. If it is `NULL`, the function will automatically generate a title.
`interpolate_len` | An integer. It specifies how many values need to be interpolated between two concentrations. It is used to control the smoothness of the synergy surface.
`col_range` | A vector of two integers. They specify the starting and ending concentration of the drug on x-axis. Use e.g., c(1, 3) to specify that only from 1st to 3rd concentrations of the drug on x-axis are used. By default, it is NULl so all the concentrations are used.
`row_range` | A vector of two integers. They specify the starting and ending concentration of the drug on y-axis. Use e.g., c(1, 3) to specify that only from 1st to 3rd concentrations of the drug on y-axis are used. By default, it is NULl so all the concentrations are used.
`dynamic` | A logical value. If it is `TRUE`, this function will use plot_ly to generate an interactive plot. If it is `FALSE`, this function will use wireframe to generate a static plot.
`grid` | A logical value. It indicates whether to add grids on the surface.
`high_value_color` | An R color value. It indicates the color for the high values.
`low_value_color` | An R color value. It indicates the color for low values.
`text_size_scale` | A numeric value. It is used to control the size of text in the plot. All the text size will multiply by this scale factor.

### Value

If `dynamic = FALSE`, this function will return a plot project recorded by recordPlot. If `dynamic = FALSE`, this function will return a plotly plot object.

### Author(s)

- Shuyu Zheng shuyu.zheng@helsinki.fi

- Jing Tang jing.tang@helsinki.fi

### Examples

    data("mathews_screening_data")
    data <- ReshapeData(mathews_screening_data)
    Plot2DrugSurface(data)
    Plot2DrugSurface(data, dynamic = TRUE)

[Package synergyfinder version 3.0.14 Index]