PlotDoseResponse {synergyfinder} | R Documentation

## Visualize the Drug Combination Dose-response Data

### Description

A function to visualize the drug combination dose-response data

### Usage

    PlotDoseResponse(
      data,
      block_ids = c(1),
      drugs = c(1, 2),
      adjusted = TRUE,
      statistic = NULL,
      summary_statistic = "mean",
      high_value_color = "#A90217",
      low_value_color = "#2166AC",
      point_color = "#C24B40",
      curve_color = "black",
      text_size_scale = 1,
      heatmap_text_label_size_scale = 1,
      heatmap_text_label_color = "#000000",
      curve_plot_title = NULL,
      heatmap_plot_title = NULL,
      Emin = NA,
      Emax = NA,
      save_file = FALSE,
      file_type = "pdf",
      file_name = NULL,
      width = 12,
      height = 6
    )

### Arguments

`data` | A list object generated by function `ReshapeData`.
`block_ids` | A vector of characters/integers or NULL. It contains the block IDs for the blocks to visualize. By default, it is NULL so that the visualization of all the drug combinations in input `data`.
`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`.
`adjusted` | A logical value. If it is `FALSE`, original response matrix will be plotted. If it is `TRUE`, adjusted response matrix will be plotted.
`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.
`summary_statistic` | A vector of characters or NULL. It indicates the summary statistics printed in heatmap 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 print different sample quantile. For example quantile_50 equal to median. If it is `NULL`, no statistics will be printed.
`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.
`point_color` | An R color value. It indicates the color for points in dose response curve plots.
`curve_color` | An R color value. It indicates the color for curves in dose response curve plots.
`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.
`heatmap_text_label_size_scale` | A numeric value. It is used to control the size of text labels in the heatmap plot. It only works while `plot_type = "heatmap"`.
`heatmap_text_label_color` | NULL or an R color value. It is used to control the color of text labels in the heatmap plot. If it is `NULL`, text label will not be shown.It only works while `plot_type = "heatmap"`.
`curve_plot_title` | A character value to indicate the plot title for the dose-response curve.
`heatmap_plot_title` | A character value to indicate the plot title for the heatmap.
`Emin` | A numeric or `NA`. the minimal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Default setting is `NA`.
`Emax` | A numeric or `NA`. the maximal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Default setting is `NA`.
`save_file` | A parameter to specify if the visualization results are saved as pdf files in current working directory or not. If it is FALSE, the results are returned as a list of the plots. It is FALSE by default.
`file_type` | A character. It indicates the format of files you want to save as. Default is "pdf". Available values are "jpeg", "bmp", "png", "tiff", "pdf", "svg".
`file_name` | A character vector. It indicates the file names, if user chose to save the plot to local directory.If it is not defined by user, a default name will be assigned.
`width` | a numeric value. It indicates the width of saved file.
`height` | a numeric value. It indicates the height of saved file.

### Value

A list of plot objects recorded by recordPlot. The plot will be saved into a local file if `save_file = TRUE`. If `save_file = FALSE`, the plot will be printed in default graphic device.

### Author(s)

- Shuyu Zheng shuyu.zheng@helsinki.fi

- Jing Tang jing.tang@helsinki.fi

### Examples

    ## Not run:
    data("mathews_screening_data")
    data <- ReshapeData(mathews_screening_data)
    plots <- PlotDoseResponse(data)

    ## End(Not run)

[Package synergyfinder version 3.0.14 Index]