# CCplot: Concordance Correlation Plot In nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

## Description

Plotting function for reliability measure.

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```CCplot( method1, method2, Ptype = "None", metrics = FALSE, xlabel = "", ylabel = "", title = "", subtitle = NULL, xrange = NULL, yrange = NULL, MArange = c(-3.5, 5.5) ) ```

## Arguments

 `method1` measurements obtained in batch 1 or using method 1 `method2` measurements obtained in batch 2 or using method 2 `Ptype` type of plot to be outputted c("scatter", "MAplot") `metrics` if `TRUE`, prints Rc, Ca, and R2 to console `xlabel` x-axis label for scatterplot `ylabel` y-axis label for scatterplot `title` title for the main plot `subtitle` subtitle of plot `xrange` range of x axis `yrange` range of y axis `MArange` MA range

## Value

Either a scatterplot or MA plot showing concordance correlation.

Aline Talhouk

Aline Talhouk

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30``` ```# Simulate normally distributed data set.seed(12) a1 <- rnorm(20) + 2 a2 <- a1 + rnorm(20, 0, 0.15) a3 <- a1 + rnorm(20, 0, 0.15) + 1.4 a4 <- 1.5 * a1 + rnorm(20, 0, 0.15) a5 <- 1.3 * a1 + rnorm(20, 0, 0.15) + 1 a6 <- a1 + rnorm(20, 0, 0.8) # One scatterplot CCplot(a1, a2, Ptype = "scatter") m2 <- list(a1, a2, a3, a4, a5, a6) mains <- c("Perfect Agreement", "Very Good Agreement", "Location Shift", "Scale Shift", "Location and Scale Shift", "Measurement Error") subs <- letters[1:6] par(mfrow = c(3, 2), mar = c(5.1, 4.1, 1.5, 1.5)) # Scatterplots mapply(function(y, t, s) CCplot(method1 = a1, method2 = y, Ptype = "scatter", xlabel = "X", ylabel = "Y", title = t, subtitle = s), y = m2, t = mains, s = subs) # MAplots and show metrics mapply(function(y, t, s) CCplot(method1 = a1, method2 = y, Ptype = "MAplot", title = t, subtitle = s, metrics = TRUE), y = m2, t = mains, s = subs) ```

nanostringr documentation built on Feb. 6, 2021, 5:05 p.m.