plotCCC: Calculates Concordance Correlation Coefficient (CCC) to...

In nickytong/GenAnalysis: Genomic Analysis

Description

This function calculates and plots concordance for paired data.

Usage

plotCCC(x, y, labels = NULL, cols = NULL, cexlab = 0.8,
  colab = "purple", poslab = 1, xlab = NA, ylab = NA, tag = "",
  col_legend = "red", pch = 20, main = NA, cex = 2, plot = TRUE,
  ylim = NA, xlim = NA, maskBeyondLim = FALSE, plotOutlier = FALSE,
  sampleName = NA, alpha_outlier = 0.01, show = c("identity", "h0", "v0"))

Arguments

x	x vector
y	y vector
cols	color vector for the points
xlab	xlab
ylab	ylab
tag	add a tag
pch	pch of the points
main	main title
cex	for the dots
plot	whether draw a figure
maskBeyondLim	whether mask values beyond xlim (for x) or ylim (for y) when xlim and ylim is specified. Default is FALSE so that even xlim ylim specified, CCC will not be affected
plotOutlier	logical whether add an outlier plot comparing Diff vs Mean plot and related statistics
sampleName	symbols of the text to be shown in outlier plot
alpha_outlier	alpha to call outliers based on the observed differences assuming from Normal(mean_diff, sd_diff)
cex.main	cex for main title
cex.legend	cex for legend text

Details

This function calls the epi.ccc() function from epiR package for the calculation.

infinite values in x and y are masked as NA so as to compute CCC and corr (otherwise, result becomes nan).

Value

a vector of c('ccc', 's_shift', 'l_shift', 'ccc_lo', 'ccc_hi', 'Cb', 'corr'). s_shift is scale shift; l_shift is location shift; ccc_lo and ccc_hi represent 95 Pearson correlation

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.