PlotMultiDrugSurface: 3D Plot for Multi-drug Combination Dose-Response/Synergy...

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

3D Plot for Multi-drug Combination Dose-Response/Synergy Scores

Description

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.

Usage

PlotMultiDrugSurface(
  data,
  plot_block = 1,
  plot_value = "response",
  summary_statistic = NULL,
  plot_title = NULL,
  distance_method = "mahalanobis",
  high_value_color = "#FF0000",
  low_value_color = "#00FF00",
  show_data_points = TRUE,
  point_color = "#DDA137",
  text_size_scale = 1,
  axis_line = FALSE,
  colorbar_tick = FALSE,
  x_range = NULL,
  y_range = NULL,
  z_range = NULL,
  color_range = NULL,
  camera_width = NULL,
  camera_height = NULL,
  camera_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.
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.
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 "mahalanobis".
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.
axis_line	A logical value. Whether to show the axis lines and ticks.
colorbar_tick	A logical value. Whether to show the ticks on color bar.
x_range	A numeric vector with two values or NULL. It is used to set the range of x axis (coordinate 1). For example, c(-5, 5) means coordinate 1 ranges from -5 to 5 in the plot. Default value is NULL. The function automatically set the range.
y_range	A numeric vector with two values or NULL. It is used to set the range of y axis (coordinate 2). For example, c(-5, 5) means coordinate 2 ranges from -5 to 5 in the plot. Default value is NULL. The function automatically set the range.
z_range	A vector of two numeric values. They specify the range of z-axis plotted.Default value is NULL. The function automatically set the range.
color_range	A vector of two numeric values. They specify the range of the color bars. The first item (lower bounder) must be less than the second one (upper bounder). The plotted values larger than defined upper bounder will be filled in color high_value_color. The plotted values less than defined lower bounder will be filled in color low_value_color. If the defined range includes 0, value 0 will be filled in color "white". By default, it is set as NULL which means the function will automatically set the color range according to the plotted values.
camera_width	A numeric value or NULL. It indicates the output figure's width on pixel.
camera_height	A numeric value or NULL. It indicates the output figure's height on pixel.
camera_scale	A numeric value. The output plot while clicking the camera button.will multiply title/legend/axis/canvas sizes by this factor.

Value

A plotly plot object.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

Examples

data("NCATS_screening_data")
data <- ReshapeData(NCATS_screening_data)
p <- PlotMultiDrugSurface(
  data,
  plot_block = 1,
  plot_value = "response",
  show_data_points = TRUE,
  distance_method = "mahalanobis",
  summary_statistic = "mean"
)
p

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