An R package to quantify radial bridge images
cranium
depends on XQuartz
, which is not on CRAN. You can download from https://www.xquartz.org/. After install XQuartz
, restart your R and continue cranium
installation.
cranium
depends on thehdf5r
package for reading HDF5 files. You could download hdf5r
from CRAN.
install.packages("hdf5r")
If you have trouble downloading hdf5r
, the alternative is rhdf5
package. However, rhdf5
package is not available on CRAN--it is a bioconductor package. You must install it from Bioconductor. To install the package, you have to run the following code once:
install.packages("BiocInstaller",
repos = "http://bioconductor.org/packages/3.4/bioc")
source("https://bioconductor.org/biocLite.R")
biocLite("rhdf5")
If you are having trouble downloading rhdf5
using the code above, an alternative option would be downloading rhdf5
from bioconductor using the pak
package: https://github.com/r-lib/pak. Also, check the most recent version of Bioconductor here: http://bioconductor.org/about/removed-packages/.
Note that you do not have to download rhdf5
if you successfuly downloaded hdf5r
.
After installing rhdf5
or hdf5r
, you can install cranium
from GitHub using the following commands:
install.packages("devtools")
devtools::install_github("beanumber/cranium")
Library cranium
package everytime you start your R session.
library(cranium)
To download sample data, You Too and WildType, you can run:
youtoo <- download_youtoo_data("folder") #where folder is the location you want to store the You Too data
wildtype <- download_wildtype_data("folder") #where folder is the location you want to store the Wild Type data
youtoo[[1]] #first you too data sample
Once the above is ran, the files are saved in a list and in the folder you set, each data sample can be indivudually picked from list by indexing.
Now, you can simply point to a raw HDF5 file, and quickly render a 3D image of the data, along with our model of it.
file <- "~/Data/barresi/AT_1_Probabilities.h5"
library(cranium)
library(tidyverse)
tidy_brain <- file %>%
read_h5() %>%
tidy()
plot3d(tidy_brain)
A quadratic model y = x^2+x is used to fit the data. You can evaluate the quadratic model fit on your sample. The default threshold for signal frequency is 0.9.
file%>%
read_h5()%>%
qmodel.brain()
If you are working with You-Too sample, you can change the data type and the default threshold for You-Too sample is 0.5. You can also adjust the threshold.
file%>%
read_h5()%>%
qmodel.brain(type="youtoo", threshold = 0.8)
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