exir.vis: Visualization of ExIR results

View source: R/functions.R

exir.visR Documentation

Visualization of ExIR results

Description

This function has been developed for the visualization of ExIR results. Some of the documentations of the arguments of this function have been adapted from ggplot2 package. A shiny app has also been developed for Running the ExIR model, visualization of its results as well as computational simulation of knockout and/or up-regulation of its top candidate outputs, which is accessible using the 'influential::runShinyApp("ExIR")' command. You can also access the shiny app online at https://influential.erc.monash.edu/.

Usage

exir.vis(
  exir.results,
  synonyms.table = NULL,
  n = 10,
  driver.type = "combined",
  biomarker.type = "combined",
  show.drivers = TRUE,
  show.biomarkers = TRUE,
  show.de.mediators = TRUE,
  show.nonDE.mediators = TRUE,
  basis = "Rank",
  label.position = "top",
  nrow = 1,
  dot.size.min = 2,
  dot.size.max = 5,
  type.color = "viridis",
  stroke.size = 1.5,
  stroke.alpha = 1,
  dot.color.low = "blue",
  dot.color.high = "red",
  legend.position = "bottom",
  legend.direction = "vertical",
  legends.layout = "horizontal",
  boxed.legend = TRUE,
  show.plot.title = TRUE,
  plot.title = "auto",
  title.position = "left",
  plot.title.size = 12,
  show.plot.subtitle = TRUE,
  plot.subtitle = "auto",
  subtitle.position = "left",
  y.axis.title = "Feature",
  show.y.axis.grid = TRUE
)

Arguments

exir.results

An object of class "ExIR_Result" which is the output of the function "exir".

synonyms.table

(Optional) A data frame or matrix with two columns including a column for the used feature names in the input data of the "exir" model and the other column their synonyms. Note, the original feature names should always come as the first column and the synonyms as the second one. For example, if the original feature names used for running the "exir" model are Ensembl gene symbols, you can use their HGNC synonyms in the second column to be used for the visualization of the ExIR results

n

An integer specifying the number of top candidates to be selected from each category of ExIR results (default is set to 10).

driver.type

A string specifying the type of drivers to be used for the selection of top N candidates. The possible types include "combined" (meaning both driver types), "accelerator" and "decelerator" (default is set to "combined").

biomarker.type

A string specifying the type of biomarkers to be used for the selection of top N candidates. Possible types include "combined" (meaning both biomarker types), "up-regulated" and "down-regulated" (default is set to "combined").

show.drivers

Logical scalar, whether to show Drivers or not (default is set to TRUE).

show.biomarkers

Logical scalar, whether to show Biomarkers or not (default is set to TRUE).

show.de.mediators

Logical scalar, whether to show DE-mediators or not (default is set to TRUE).

show.nonDE.mediators

Logical scalar, whether to show nonDE-mediators or not (default is set to TRUE).

basis

A string specifying the basis for the selection of top N candidates from each category of the results. Possible options include "Rank" and "Adjusted p-value" (default is set to "Rank").

label.position

By default, the labels are displayed on the top of the plot. Using label.position it is possible to place the labels on either of the four sides by setting label.position = c("top", "bottom", "left", "right").

nrow

Number of rows of the plot (default is set to 1).

dot.size.min

The size of dots with the lowest statistical significance (default is set to 2).

dot.size.max

The size of dots with the highest statistical significance (default is set to 5).

type.color

A character string or function indicating the color palette to be used for the visualization of different types of candidates. You may choose one of the Viridis palettes including "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"), "viridis" (or "D", the default option) and "cividis" (or "E"), use a function specifying your desired palette, or manually specify the vector of colors for different types.

stroke.size

The size of stroke (border) around the dots (default is set to 1.5).

stroke.alpha

The transparency of the stroke (border) around the dots which should be a number between 0 and 1 (default is set to 1).

dot.color.low

The color to be used for the visualization of dots (features) with the lowest Z-score values (default is set to "blue").

dot.color.high

The color to be used for the visualization of dots (features) with the highest Z-score values (default is set to "red").

legend.position

The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector). The default is set to "bottom".

legend.direction

Layout of items in legends ("horizontal" or "vertical"). The default is set to "vertical".

legends.layout

Layout of different legends of the plot ("horizontal" or "vertical"). The default is set to "horizontal".

boxed.legend

Logical scalar, whether to draw a box around the legend or not (default is set to TRUE).

show.plot.title

Logical scalar, whether to show the plot title or not (default is set to TRUE).

plot.title

The plot title in the string format (default is set to "auto" which automatically generates a title for the plot).

title.position

The position of title ("left", "center", or "right"). The default is set to "left".

plot.title.size

The font size of the plot title (default is set to 12).

show.plot.subtitle

Logical scalar, whether to show the plot subtitle or not (default is set to TRUE).

plot.subtitle

The plot subtitle in the string format (default is set to "auto" which automatically generates a subtitle for the plot).

subtitle.position

The position of subtitle ("left", "center", or "right"). The default is set to "left".

y.axis.title

The title of the y axis (features title). Default is set to "Features".

show.y.axis.grid

Logical scalar, whether to draw y axis grid lines (default is set to TRUE).

Value

A plot with the class ggplot.

See Also

exir

Other visualization functions: cent_network.vis()

Examples

## Not run: 
MyResults <- exir.results
ExIR.plot <- exir.vis(exir.results = MyResults, n = 5)

## End(Not run)

influential documentation built on Aug. 6, 2022, 9:05 a.m.