multipleRegion_plot: Multiple Regions Connection Plot

Description Usage Arguments Details Value Author(s) Examples

View source: R/multipleRegion_plot.R

Description

This function can draw connection line(s) among multiple brain regions, based on the result from funciton permkCCA_multipleRegion(...).

Usage

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multipleRegion_plot(input, significance = 0.05, regionCodeProvided = FALSE,
  view = "coronal", color = "blue", screenShot = "None")

Arguments

input

it can accept two types of argument: (1) output generated by "permkCCA_multipleRegion(...)" (with p value). (2) output generated by summary_kcca() or meanConnection() (without p value).

significance

significance level of hypothesis testing. If there is no p value in your data (i.e. only region name and region index, then set significance as NA)

regionCodeProvided

use TRUE if region code was provided in nii2RData() funciton and FALSE if not.

view

view of brain to see. One can choose coronal, axial, SL, or SR.

color

color of dots and lines. User can specify multiple colors in this argument and the function will use these colors periodically.

screenShot

whether to save figure as png. If it is "None", then the figure will not be saved; If it is a name, for example, "plot.png", then it will be saved as "plot.png".

Details

If you provide an input with multiple patients, the function will ask you to specify which patients data you would like to use.

Value

1-4 view(s) (depends on the number of views user would like to see) of brain graphic network. All significant regions are connected by colored lines.

Author(s)

Xubo Yue, Chia-Wei Hsu (tester), Jian Kang (maintainer)

Examples

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#It will take more than 3 min to run
#write data into temp file
filePath <- tempdir()
#the nii.gz fMRI imaging file is created (toy example)
oro.nifti::writeNIfTI(brainKCCA::input_img, paste(filePath, "/",  "temp", sep=""))
#read fMRI data
testcase1 <- nii2RData(niiFile1 = "temp", resolution = "3mm", imgPath = filePath)
result1<-permkCCA_multipleRegion(imageDat = testcase1, region = c(1,5,10))
multipleRegion_plot(result1, view="axial")

neuroconductor/brainKCCA documentation built on Feb. 9, 2020, 10:23 a.m.