Giotto: comprehensive toolbox for spatial data analysis

Giotto 📄 Dries, Ruben, et al. “Giotto: a toolbox for integrative analysis and visualization of spatial expression data.” Genome biology 22 (2021): 1-31.

🔗 Homepage: https://giottosuite.readthedocs.io/en/master/ {.prompt-tip}

Installation

Requirements

• R (>= 3.5.1)
• Python (>= 3.0)
• Windows, MacOS or Linux specific installation tools

R 이랑 Python 둘 다 필요하니 명심하자

step01. Install Giotto R packages

prerequisites

• a major dependency terra needs GDAL (>= 2.2.3), GEOS (>= 3.4.0), PROJ (>= 4.9.3), sqlite3 on linux

설치 돼있는지 먼저 확인

gdal-config --version #GDAL
geos-config --version #GEOS
proj --version #PROJ
sqlite3 --version #sqlite3

Install Terra

• 🔗Terra github page

👇GDAL/GEOS/PROJ/SQLite3 설치는 여기 참조

🔗GDAL, GEOS, PROJ installation from source code without sudo permission

install.packages('terra', repos='https://rspatial.r-universe.dev')

Install Giotto

# install.packages("pak")
pak::pak("drieslab/Giotto")

Install magick

🚨ERROR: dependency ‘magick’ is not available for package ‘Giotto’

wget https://imagemagick.org/archive/ImageMagick.tar.gz
tar -xvzf ImageMagick.tar.gz 
cd ImageMagick-7.1.1-36
./configure --prefix=/source/ImageMagick-7.1.1-36/
make -j 10 & make install

# update ~/.bash_profile
PATH=/source/ImageMagick-7.1.1-36/bin:$PATH
LD_LIBRARY_PATH=/source/ImageMagick-7.1.1-36/lib:$LD_LIBRARY_PATH
PKG_CONFIG_PATH=/source/ImageMagick-7.1.1-36/lib/pkgconfig:$PKG_CONFIG_PATH

install.packages("magick")

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