PlotMultiDrugSurface: 3D Plot for Multi-drug Combination Dose-Response/Synergy...
In synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

Description Usage Arguments Value Author(s) Examples

This function will generate a dynamic 3D plot response values or synergy scores for all the observed data points in a multi-drug combination block. The concentrations of drugs will be projected to 2 dimensions and plot along x an y axis. A surface for the selected plot_value and points for all the concentration combinations will be plotted.

PlotMultiDrugSurface(
  data,
  plot_block = 1,
  plot_value = "response",
  statistic = NULL,
  summary_statistic = NULL,
  plot_title = NULL,
  distance_method = "mahalanobis",
  high_value_color = "#A90217",
  low_value_color = "#2166AC",
  show_data_points = TRUE,
  point_color = "#DDA137",
  text_size_scale = 1,
  camera_width = 500,
  camera_height = 500,
  camera_scale = 1
)

`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 predicted 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.
`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% confidence interval. If it is `NULL`, no statistics will be printed.
`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; 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 charactor value. It specifies the plot title. If it is `NULL`, the function will automatically generate a title.
`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 "euclidean".
`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.
`show_data_points`	A logical value. If it is `TRUE`, the raw data points will be shown on the plot. If it is `FALSE`, no points will be plotted.
`point_color`	An R color value. It indicates the color for data points.
`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.
`camera_width`	A numeric value. It indicates the output figure's width in pixel while clicking the camera button.
`camera_height`	A numeric value. It indicates the output figure's height in pixel while clicking the camera button.
`camera_scale`	A numeric value. The output plot while clicking the camera button.will multiply title/legend/axis/canvas sizes by this factor.

A plotly plot object.

Shuyu Zheng shuyu.zheng@helsinki.fi
Jing Tang jing.tang@helsinki.fi

data("NCATS_10023_data")
data <- ReshapeData(NCATS_10023_data)
p <- PlotMultiDrugSurface(
  data,
  plot_block = 1,
  plot_value = "response",
  statistic = NULL,
  show_data_points = TRUE
)
p