GenerateSurface: 3D Surface Plot for Nulti-drug Combination...

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

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

Description

This function will generate a surface plot for multi-drug combinations from the output of DimensionReduction. It is an auxiliary function for PlotMultiDrugSurface

Usage

GenerateSurface(
  dim_reduced_data,
  high_value_color,
  low_value_color,
  show_data_points = TRUE,
  point_color,
  plot_title,
  plot_subtitle,
  legend_title,
  z_axis_title,
  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

dim_reduced_data	A list of data frame. It contains the dimension reduced data for all the data points and other information for plotting. It is the output of DimensionReduction (combination of concentrations). It is
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.
plot_title	A character value. It is the title for plot.
plot_subtitle	A character value. It is the subtitle for plot.
legend_title	A character value. It is the title for legend.
z_axis_title	A character value. It is the title for z-axis.
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 will multiply title/legend/axis/canvas sizes by this factor.

Value

A ggplot object.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

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