scatter: scatter - XY scatter plot with extra information

In corto: Inference of Gene Regulatory Networks

scatter - XY scatter plot with extra information

Description

This function will plot two variables (based on their common names), calculate their Coefficient of Correlation (CC), plot a linear regression line and color the background if the correlation is positive (red), negative (blue) or non-significant (white)

Usage

scatter(
  x,
  y,
  method = "pearson",
  threshold = 0.01,
  showLine = TRUE,
  grid = TRUE,
  bgcol = FALSE,
  pch = 20,
  subtitle = NULL,
  extendXlim = FALSE,
  ci = FALSE,
  ...
)

Arguments

x	The first named vector
y	The second named vector
method	a character string indicating which correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman": can be abbreviated.
threshold	a numeric value indicating the significance threshold (p-value) of the correlation, in order to show a colored background. Default is 0.01.
showLine	a boolean indicating if a linear regression line should be plotted. Default is TRUE
grid	a boolean indicating whether to show a plot grid. Default is TRUE
bgcol	Boolean. Should a background coloring associated to significance and sign of correlation be used? Default is TRUE, and it will color the background in red if the correlation coefficient is positive, in blue if negative, in white if not significant (accordin to the _threshold_ parameter)
pch	the _pch_ parameter indicating the points shape. Default is 20
subtitle	NULL by default, in which case the function will print as a subtitle the correlation coefficient (CC) and its pvalue. Otherwise, a user-provided string, bypassing the predefined subtitle
extendXlim	logical. If TRUE, the x-axis limits are extended by a fraction (useful for labeling points on the margins of the plot area). Default is FALSE
ci	logical. If TRUE, confidence intervals of linear regression are shown at 95 percent confidence.
...	Arguments to be passed to the core _plot_ function (if a new plot is created)

Value

A plot

Examples

x<-setNames(rnorm(200),paste0("var",1:200))
y<-setNames(rnorm(210),paste0("var",11:220))
scatter(x,y,xlab="Variable x",ylab="Variable y",main="Scatter plot by corto package",ci=TRUE)

corto documentation built on March 31, 2023, 9:25 p.m.