lakerwsl / rkcolocal Goto Github PK
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This is an R package for colocalization analysis.
Hello!
I would like to try out the RKColocal package and especially the SACA feature on some data of mine. I've tried some basic functions of the package as described here, and plotting, calculating classical colocalisation measures and statistical testing works
>
> library("RKColocal")
Loading required package: pcaPP
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: EBImage
Loading required package: abind
Attaching package: ‘abind’
The following object is masked from ‘package:EBImage’:
abind
Loading required package: grid
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: rJava
> img = readImage('./R/PKColoc/sample.tif')
> X = as.matrix(imageData(img)[,,,1])
> Y = as.matrix(imageData(img)[,,,2])
> MKTK = colocalroi(X, Y, Thresholds=NULL, method = 'trunkendall')
> colocalplot(X, Y, method = 'scatter')
> Testresult <- colocalroitest(X, Y, method = 'pearson')
> Testresult
$Index_Value
[1] 0.182037
$P_value
[1] 0.00990099
$Null_Distribution
[1] -1.245085e-04 1.119805e-03 9.935908e-04 -1.098348e-03 -2.223630e-03
[6] 4.452810e-05 -2.958354e-03 7.083850e-04 -5.261125e-04 -4.332244e-04
[11] -3.669074e-04 -1.422903e-03 -1.202266e-03 1.131156e-03 2.185694e-03
[16] 1.158986e-03 -2.378240e-03 -1.786250e-03 -3.392983e-04 2.794160e-04
[21] -8.482628e-04 -1.469153e-03 -3.335707e-03 -3.026556e-03 9.270906e-04
[26] -1.284819e-03 -2.052960e-03 1.654883e-03 -2.015031e-03 -1.284514e-03
[31] 2.467403e-03 -4.691156e-04 2.337849e-04 -7.895867e-04 -1.203076e-03
[36] -2.067944e-03 -1.583085e-03 2.733935e-04 1.019337e-03 3.778610e-04
[41] 9.955983e-04 2.122941e-03 -1.779907e-03 3.935396e-04 1.187542e-03
[46] 3.799560e-03 1.671073e-03 -3.713423e-04 -3.783648e-04 -2.882320e-03
[51] -2.035717e-03 2.995917e-03 5.714077e-04 -1.172035e-04 2.436107e-03
[56] -4.288277e-04 -2.999619e-03 5.150444e-04 2.010081e-04 3.628619e-04
[61] 2.632184e-04 -2.117709e-04 1.183359e-03 3.780290e-04 -9.232816e-04
[66] 9.960258e-04 -1.529294e-03 -1.177359e-03 -3.043059e-03 -2.606919e-04
[71] 7.932277e-04 -1.740527e-03 1.163788e-03 -3.702359e-03 1.945279e-03
[76] -4.389340e-04 -1.118767e-03 -1.284903e-03 -5.272880e-04 7.217354e-04
[81] 2.889537e-05 -6.231301e-04 1.856055e-03 -5.682629e-04 -8.361337e-04
[86] -1.445291e-03 2.392617e-05 -1.082212e-03 9.980791e-04 -1.109214e-04
[91] -1.602779e-03 -1.851727e-03 3.447884e-03 -2.676468e-03 -3.307072e-05
[96] -2.006875e-04 -3.135810e-03 3.915435e-05 -9.880873e-04 2.567245e-03
attr(,"class")
[1] "colocalroitest"
However as soon as I run saca <- colocalpixel(X, Y) str(saca)
I get a fatal error of R and it crashes. I'm running the newest version of R and RStudio on MacOS ARM64 and installed RKColocal V2 from the tar.gz provided on this repository. The image I am using is a 8bit two color tif > dim(img) [1] 1380 1380 2
Thank you!
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