plotCor: scatter plot with correlation statistics

In raim/segmenTools: Tools for Functional Genome Exploration

scatter plot with correlation statistics

Description

scatter plot with correlation statistics

Usage

plotCor(
  x,
  y,
  outliers,
  cor.method = c("pearson", "kendall", "spearman"),
  line.methods = c("ols", "tls"),
  na.rm = TRUE,
  circular = FALSE,
  circular.jitter = "",
  cor.legend = TRUE,
  line.legend = FALSE,
  title = FALSE,
  line.col = c(1, 2),
  pch = 20,
  cex = 1,
  legpos,
  legbg = "#FFFFFF99",
  legcex = cex,
  signif = 1,
  round = 2,
  density = TRUE,
  col,
  ...
)

Arguments

x	the x coordinates of the points in the plot.
y	the y coordinates of the points in the plot.
outliers	vector of indices or logical vector of x,y values to exclude from correlation analysis.
cor.method	method to calculate correlation and p-value via cor.test.
line.methods	regression line methods, where "ols" is a linear regression (ordinary least squares) with R's lm and "tls" (total least squares) is calculated manually via eigen and cov.
na.rm	remove NA values from x and y.
circular	treat data as circular, NOT fully implemented/tested.
circular.jitter	hack for equispaced phases (for circular=TRUE), adds jitter to x or y (arguments circular.jitter=c('x','y')) to avoid NA in cor.circular.
cor.legend	plot correlation, p-value and slope (TLS) as a legend.
line.legend	plot line fit method as a legend.
title	plot correlation parameters (as in legend) on the top of the plot.
line.col	colors of the regression lines drawn with line.methods. ## @param line.type line types of the regression lines drawn with ## line.methods.
pch	point symbols.
cex	point size.
legpos	position of the legend.
legbg	background color of the legend, default: transparent via alpha=0. ## @param col color(s) of plotted points, if density=FALSE, or ## color palette function if density=TRUE (argument ## colf to dense2d).
legcex	font size (cex) of the legend.
signif	number of digits to be shown for p-values in the plot legend (argument digits to signif.
round	number of decimal places to be shown for correlation values in the plot legend (argument digits to round.
density	indicate local point densities by using dense2d instead of the base plot function.
col	point color if density==FALSE.
...	further arguments to the plotting function; plot or, if density=TRUE, dense2d.

raim/segmenTools documentation built on Feb. 16, 2025, 10:40 p.m.