glXYPlot: Glimma XY Plot

In Shians/Glimma: Interactive HTML graphics

Description

Draw an interactive XY plot with multiple panels

Usage

glXYPlot(
  x,
  y,
  counts = NULL,
  groups = NULL,
  samples = NULL,
  status = rep(0, nrow(data)),
  anno = NULL,
  display.columns = NULL,
  xlab = "x",
  ylab = "y",
  side.main = "GeneID",
  side.xlab = "Group",
  side.ylab = "Expression",
  sample.cols = rep("#1f77b4", length(groups)),
  cols = c("#00bfff", "#858585", "#ff3030"),
  jitter = 30,
  path = getwd(),
  folder = "glimma-plots",
  html = "XY-Plot",
  launch = TRUE,
  ...
)

Arguments

x	a numeric vector of values to plot on the x-axis of the summary plot.
y	a numeric vector of values to plot on the y-axis of the summary plot.
counts	the matrix containing all counts, the column order should correspond to the order of the x and y vectors.
groups	the factor containing experimental groups of the samples.
samples	the names of the samples.
status	vector giving the control status of data point, of same length as the number of rows of object. If NULL, then all points are plotted in the default colour
anno	the data.frame containing gene annotations.
display.columns	character vector containing names of columns to display in mouseover tooltips and table.
xlab	the label on the x axis for the left plot.
ylab	the label on the y axis for the left plot.
side.main	the column containing mains for right plot.
side.xlab	the label on the x axis for the right plot.
side.ylab	the label on the y axis for the right plot.
sample.cols	vector of strings denoting colours for each sample point on the expression plot.
cols	vector of strings denoting colours corresponding to control status -1, 0 and 1. (may be R named colours or Hex values)
jitter	the amount of jitter to apply to the samples in the expressions plot.
path	the path in which the folder will be created.
folder	the name of the fold to save html file to.
html	the name of the html file to save plots to.
launch	TRUE to launch plot after call.
...	additional arguments to be passed onto the MD plot. (main, etc. can be set for the left plot)

Value

Draws a two-panel interactive XY scatter plot in an html page. The left plot shows the x and y values specified. The right plot shows the expression levels of a particular gene in each sample. Hovering over points on left plot will plot expression level for the corresponding gene, clicking on points will fix the expression plot to that gene. Clicking on rows on the table has the same effect as clicking on the corresponding gene in the plot. This function generates a display that is similar in style to glMDPlot, except that it provides more flexibility in what the user can provide.

Author(s)

Charity Law and Shian Su

Examples

data(iris)

glXYPlot(iris$Sepal.Width, iris$Sepal.Length, 
         xlab="Sepal.Width", ylab="Sepal.Length", side.main="PlantID")

Shians/Glimma documentation built on April 1, 2020, 5:46 a.m.