general.corplot: Function to create a correlation plot.

Description Usage Arguments Value Author(s) Examples

Description

The upper diagonale of the correlation matrix is visualized by colored ellipses, with the color, shape and direction of the ellipsis showing the dependence of the respective variable pair. the lower diagonale of the matrix-like plot contains the corresponding correlation values.

Usage

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general.corplot(data, cor.type = c("pearson", "spearman", "kendall"),
  col = c("tomato1", "green3"), plot.type = c("ellipse", "points"),
  size.cor = 1, add.hist = FALSE, disp.sig.lev = 1, disp.thresh = 0.1,
  conf.level = NULL, n.boot = 1000, pt.size = 0.4, group.cut = NULL,
  border = NA, png.out = FALSE, png.width = 5, png.height = 5,
  file.name = NULL, ...)

Arguments

data

data set in wide format (Required)

cor.type

type of correlation coefficient, 'pearson', 'spearman' or 'kendall' (Default: 'spearman')

col

vector of length two with the colors for negative and positive correlations (Default: c('tomato1','green3'))

plot.type

plot type in the upper diagonale, 'ellipse' or 'points', i.e. scatterplots (Default='ellipse')

size.cor

text size of the correlation numbers (Default: 1)

add.hist

add histograms on the left hand side of the plot (Defaul=FALSE)

disp.sig.lev

ellipses of correlations with a p-value above this threshold will not be displayed and the corresponding correlation number will be displayed in grey (Default: 1)

disp.thresh

ellipses of correlations with an absolute value below this threshold will not be displayed

conf.level

level for the confidence intervals (Does not work for 'kendall') (Default: Null)

n.boot

number of bootstrap iterations, if confidence intervals for 'cor.type='spearman” are calculated (Default: 1000)

pt.size

size of the points, if plot.type='points' (Default: 0.4)

group.cut

number of the last variable in the first group if variables can be split up into two groups,

border

color of the border around the ellipses (Default: NA)

png.out

output as PNG? (Default: FALSE)

png.width

width of PNG in inches (Default: 5)

png.height

height of PNG in inches (Default: 5)

file.name

filename of the PNG without '.png'

...

Additional parameters for par()

Value

The correlation plot

Author(s)

Sebastian Voss, Adam Skubala

Examples

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## Not run: 
data(mtcars)
general.corplot(data=mtcars, cor.type='pearson', disp.sig.lev=0.05, group.cut=3)
general.corplot(data=mtcars, cor.type='pearson', disp.sig.lev=0.05, cex=0.95)
general.corplot(data=mtcars, cor.type='pearson', disp.sig.lev=0.05, group.cut=4, 
                conf.level=0.95, cex=0.95)
general.corplot(data=mtcars, cor.type='pearson', disp.sig.lev=0.05, group.cut=4, 
                plot.type='points', conf.level=0.95, cex=0.95)
general.corplot(data=mtcars, cor.type='pearson', disp.thresh=0.5, group.cut=4,
                plot.type='points', conf.level=0.95, cex=0.95, add.hist=TRUE)

## End(Not run)

jhooge/BioViz documentation built on May 19, 2019, 9:28 a.m.