PlotBarometer: Plot Barometer for Responses at One Data Point

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

Plot Barometer for Responses at One Data Point

Description

This function will plot a barometer. The needle will point at the response (% inhibition) at the data point specified by plot_concs. The reference additive effects calculated by different models will be marked on the bar if they are included in input data.

Usage

PlotBarometer(
  data,
  plot_block = 1,
  plot_concs,
  graduation_color = "#6C6C6C",
  needle_color = "#6C6C6C",
  needle_text_size = 5,
  needle_text_offset = 2,
  graduation_label_size = 4,
  graduation_label_offset = 0.7,
  annotation_label_size = 4,
  annotation_label_offset = 0.6,
  annotation_label_color = "#6C6C6C",
  font_family = "",
  color_bar_color = "#8f1b01",
  color_bar_outer = 9,
  color_bar_inner = 8,
  major_graduation_outer = 7.8,
  minor_graduation_inner = 7.5,
  major_graduation_inner = 7,
  show_concs = TRUE
)

Arguments

data	A list object generated by function CalculateSynergy.
plot_block	An integer or character. It indicates the block id for the combination matrix to visualize.
plot_concs	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.
graduation_color	An R color value. It indicates the color of the graduation texts and ticks.
needle_color	An R color value. It indicates the color of the needle.
needle_text_size	A numeric value. It indicates the size of the text near the center of barometer which showing the response value. The unit is "mm".
needle_text_offset	A numeric value. It is used to set the position of the response values text. Smaller value means the text is closer to the center.
graduation_label_size	A numeric value. It indicates the size of the graduation texts. The unit is "mm".
graduation_label_offset	A numeric value. It is used to set the position of graduation texts. Smaller values means the graduation texts is closer to the ticks. It ranges from 0 to 1.
annotation_label_size	A numeric value. It indicates the size of the labels for the additive effects at the out-most layer. The unit is "mm".
annotation_label_offset	A numeric value. It is used to set the position of additive effect labels. Smaller values means the labels is closer to the color bar. It ranges from 0 to 1.
annotation_label_color	An R color value. It indicates the color of the additive effects at the out-most layer.
font_family	The font family for all the texts in the plot.
color_bar_color	An R color value. It indicates the color of the largest value in the color bar.
color_bar_outer	A numerical value. It indicates the proportion of the radius for the outer side of color bar comparing to the outermost edge for plotting area. It ranges from 0 to 1.
color_bar_inner	A numerical value. It indicates the proportion of the radius for the inner side of color bar comparing to the outermost edge for plotting area. It ranges from 0 to 1.
major_graduation_outer	A numerical value. It indicates the proportion of the radius for the outer side of graduation comparing to the outermost edge for plotting area. It ranges from 0 to 1.
minor_graduation_inner	A numerical value. It indicates the proportion of the radius for the outer side of graduation comparing to the outermost edge for plotting area. It ranges from 0 to 1.
major_graduation_inner	A numerical value. It indicates the proportion of the radius for the outer side of graduation comparing to the outermost edge for plotting area. It ranges from 0 to 1.
show_concs	A logical value. If it is TRUE, the concentration of drugs will be shown on the plot.

Value

A ggplot object.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

References

Tang J, Wennerberg K and Aittokallio T (2015) hrefhttps://www.frontiersin.org/articles/10.3389/fphar.2015.00181/fullWhat is synergy? The Saariselkä agreement revisited. Front. Pharmacol. 6:181. doi: 10.3389/fphar.2015.00181

Examples

data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
data <- CalculateSynergy(data, method = c("ZIP", "HSA", "Bliss", "Loewe"))
p <- PlotBarometer(data, plot_block = 1, c(625, 50))
p

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