PlotMultiDrugBar {synergyfinder} | R Documentation

## Bar Plot for Multi-drug Combination Dose-Response/Synergy Scores

### Description

This function will generate a group of bar plots for one drug combination block. Each panel (columns) visualize the concentrations for all the drugs and metrics specified by `plot_values`. Each row represents a data point in the combination data. The data point specified by `highlight_row` will be highlighted in different color.

### Usage

    PlotMultiDrugBar(
      data,
      plot_block = 1,
      plot_value = c("response", "response_origin"),
      sort_by = "response",
      highlight_row = NULL,
      pos_value_color = "#CC3311",
      neg_value_color = "#448BD4",
      highlight_pos_color = "#A90217",
      highlight_neg_color = "#2166AC",
      panel_title_size = 10,
      axis_text_size = 10,
      highlight_label_size = 5,
      data_table = FALSE
    )

### 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.
`sort_by` | A character. It indicates by which metric the bars (data points) will be sorted. It could be one of the available values for `plot_value` or one of the concentration columns (e.g. "cocn1", "conc2", ...)
`highlight_row` | A vector of numeric values with the length same as the number of drugs in selected block. It contains the concentrations for "drug1", "drug2", ... The data point selected by these concentrations will be highlighted in the plot.
`pos_value_color` | An R color value. It indicates the color for the positive values.
`neg_value_color` | An R color value. It indicates the color for the negative values.
`highlight_pos_color` | An R color value. It indicates the highlight color for the positive values.
`highlight_neg_color` | An R color value. It indicates the highlight color for the negative values.
`panel_title_size` | A numeric value. It indicates the size of panel titles in unit "mm".
`axis_text_size` | A numeric value. It indicates the size of axis texts in unit "mm".
`highlight_label_size` | A numeric value. It indicates the size of the labels for highlighted rows in unit "mm".
`data_table` | A logic value. If it is `TRUE`, the data frame used for plotting will be output.

### Value

A ggplot object. If `data_table = TRUE`, the output will be a list containing a ggplot object and a data frame used for plotting.

### Author(s)

- Shuyu Zheng shuyu.zheng@helsinki.fi

- Jing Tang jing.tang@helsinki.fi

### Examples

    data("NCATS_screening_data")
    data <- ReshapeData(NCATS_screening_data)
    data <- CalculateSynergy(data, method = c("HSA"))
    p <- PlotMultiDrugBar(data,
      plot_block = 1,
      plot_value = c("response", "HSA_ref", "HSA_synergy"),
      highlight_row = c(0, 0, 0),
      sort_by = "HSA_synergy"
    )
    p

[Package synergyfinder version 3.0.14 Index]