MRIaggr-heatmapMRIaggr: Correlation between contrast parameters

In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description

Display a correlation map of the contrast parameters.

Usage

## S4 method for signature 'MRIaggr'
heatmapMRIaggr(object, param, num = NULL,
         rescale = TRUE, method = "pearson", points.values = TRUE, type = "image", 
		 breaks = NULL, col = cm.colors(256), main = NULL,
         mgp = c(2,0.5,0), mar = c(4,4,1,6), las = 1, cex.axis = 1,
         filename = paste(object@identifier, "heatmapMRIaggr", sep = "_"), ...)

Arguments

object	an object of class MRIaggr. REQUIRED.
param	the contrast parameters used to compute the correlations. character vector. REQUIRED.
num	the slices to use. numeric vector or NULL.
rescale	should the contrast parameters be scaled ? logical.
method	the correlation coefficient which is to be computed. Can be "pearson", "kendall" or "spearman".
points.values	should the correlation values be printed on the plot ? logical.
type	the type of plot to display. Any of "image" or "image.plot" or FALSE meaning no plot.
breaks	the break points to use to generate the color intervals. numeric vector or NULL leading to automatic breakpoints generation.
col	the colors with which the correlations will be displayed. character vector.
main	an overall title for the plot. character.
mgp	the margin line for the axis title, axis labels and axis line. positive numeric vector of size 3.
mar	the number of margin lines to be specified on the four sides of the plot. positive numeric vector of size 4.
las	the style of the axis labels. Any of 0, 1, 2 or 3.
cex.axis	the magnification to be used for axis annotation relative to the current setting of cex. positive numeric.
filename	the name of the file used to export the plot. character.
...	additional arguments to be passed to optionsMRIaggr for specifying the graphical parameters.

Details

This function with argument type set to image.plot requires to have installed the field package to work.

Arguments ... must correspond to some of the following arguments : height, hemisphere, path, res, unit, width, window.

ARGUMENTS:
Information about the num argument can be found in the details section of initNum.

If breaks is not NULL, it must be of length length(col)+1.

Information about the mar, las and mgp arguments can be found in par.

Value

None.

Examples

## load a MRIaggr object
data("MRIaggr.Pat1_red", package = "MRIaggr")

## pearson
heatmapMRIaggr(MRIaggr.Pat1_red, param = c("MASK_T2_FLAIR_t2","DWI_t0","TTP_t0","MTT_t0"),
           las = 1, type = "image", cex = 0.75,
           breaks = seq(-1, 1, length.out = 51),
           col = cm.colors(50))  	
## spearman
heatmapMRIaggr(MRIaggr.Pat1_red, param = c("MASK_T2_FLAIR_t2","DWI_t0","TTP_t0","MTT_t0"),
           las = 1, type = "image", cex = 0.75, method = "spearman",
           breaks = seq(-1, 1, length.out = 51),
           col = cm.colors(50))  


## spearman with legend
  heatmapMRIaggr(MRIaggr.Pat1_red, param = c("MASK_T2_FLAIR_t2","DWI_t0","TTP_t0","MTT_t0"),
           las = 1, type = "image.plot", cex = 0.75, method = "spearman",
           breaks = seq(-1, 1, length.out = 51),
           col = cm.colors(50))  

bozenne/MRIaggr documentation built on May 13, 2019, 1:39 a.m.