Visual Studio code
Web: https://code.visualstudio.com/.
Installation
Download and extract a copy for Linux x64, e.g., for the latest version 1.58.0,
cd ${HPC_WORK}
tar xvfz code-stable-x64-1625728370.tar.gz
ln -sf ${HPC_WORK}/VSCode-linux-x64/bin/code ${HPC_WORK}/bin/code
By default it requires chrome-sandbox is owned by root and has mode 4755
which could be achieved at CSD3 by
sudo chown root:root chrome-sandbox
sudo chmod 4755 chrome-sandbox
Unfortunately, as ordinary users this is impossible and we use without this option.
Execution
Start for reasons above,
code --no-sandbox
ceuadmin module
This is called with
module load ceuadmin/VSCode/1.76.2
which enables executation with relevant command-line arguments.
Jupyter notebook
We could start our virtual environment as described in hail
, e.g.,
cd ~/rds/results/public/gwas/ukb_exomes/tutorials
code --no-sandbox 01-genome-wide-association-study.ipynb &
which greatly simplifies the procedure as described for genebass
. MAKE sure various extensions/options suggesed from the session.
Markdown document
It will be displayed by design.
CodeGPT
From Visual Studio Code, install CodeGPT.
Supply an API key from Open AI, https://platform.openai.com/overview, entered via Ctrl-Shift-p
for CodeGPT: Set API Key
.
Create a file such as testCodeGPT.R
with comments # I would like to draw a forest plot
and key in Ctrl-Shift-i
.
Here is an example,
# Can I draw a Manhattan plot of GWAS
with answer below,
Yes, you can draw a Manhattan plot of GWAS in R using the qqman
package.
Here's a sample code:
# install and load the `qqman` package
install.packages("qqman")
library(qqman)
# read in the GWAS results file
gwas_results <- read.table("my_gwas_results.txt", header=T)
# specify the chromosome column
chr_col <- "CHR"
# specify the p-value column
pval_col <- "P_VALUE"
# draw the Manhattan plot
manhattan(gwas_results, chr=chr_col, p=pval_col)
Replace "my_gwas_results.txt"
with the actual name of your GWAS results file. Also, make sure to specify the correct column names for chromosome and p-value in chr_col
and pval_col
, respectively.