This org mode document contains the code and scripts to generate the results presented in:
Kalign 3: multiple sequence alignment of large data sets.
Programs to test:
Since the clustal papers provide a great overview of alignment programs I think these two should suffice. Note I am not comparing kalign against consistency based methods as these are a) all more accurate and b) slower. Kalign is targeted at the accurate and fast niche.
cd
mkdir -p kalignbenchmark
cd kalignbenchmark
mkdir -p data
mkdir -p programs
mkdir -p scratchcd
cd ~/kalignbenchmark/data
for idx in ${!tbl[*]}; do
#echo ${tbl[$idx]}
if [[ ${tbl[$idx]} =~ ^http* ]];
then
echo "wget ${tbl[$idx]}"
wget ${tbl[$idx]}
fi
donewget http://www.clustal.org/omega/homfam-20110613-25.tar.gz wget http://clustal.org/omega/bali3fam-26.tar.gz wget http://www.lbgi.fr/balibase/BalibaseDownload/BAliBASE_R1-5.tar.gz wget http://projects.binf.ku.dk/pgardner/bralibase/data-set1.tar.gz wget http://projects.binf.ku.dk/pgardner/bralibase/data-set2.tar.gz wget http://bioinf.ucd.ie/quantest2.tar
Unpack data sets:
cd
cd ~/kalignbenchmark/data
mkdir -p homfam
mv homfam-20110613-25.tar.gz homfam
cd homfam
tar -zxvf homfam-20110613-25.tar.gz
cd ~/kalignbenchmark/data
for filename in *.tar.gz; do
tar -zxvf $filename
done
tar -xvf quantest2.tarcd ~/kalignbenchmark/data/bb3_release/bali_score_src
gcc *.c -lm -lexpat -o bali_score
cp bali_score ~/kalignbenchmark/programs
And kalign3!
NOTE: this is manual!
Add:
#include <limits.h>
to qscore header: qscore.h
then:
make
export PATH=$HOME/kalignbenchmark/programs:$PATH
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*_test.fa" -exec rm -rf {} \;
printf "Generate commands to reformat the reference alignments\n\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.fa" -o -name '*.fasta' | grep structural | awk -v outdir="$SCRATCHDIR" '{printf "kalign %s --changename -reformat msf -o %s.msf\n", $1,$1 }' > run_reformat.sh
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.fa" -o -name '*.fasta' | grep unaligned | awk -v outdir="$SCRATCHDIR" '{printf "kalign %s --changename -reformat fasta -o %s_test.fa\n", $1,$1 }' >> run_reformat.sh
chmod 755 run_reformat.sh
./run_reformat.sh
create script to merge *_ref.vie and *_test-only.vie alignments.
<<scratchdir>>export PATH=$HOME/kalignbenchmark/programs:$PATH
DIR=`pwd`
function usage()
{
printf "This script will merge *_ref.vie and *_test-only.vie alignments and convert them into msf format.\n\n" ;
printf "usage: $0\n\n" ;
exit 1;
}
while getopts h opt
do
case ${opt} in
h) usage;;
*) usage;;
esac
done
find ~/kalignbenchmark/data/homfam -name "*_test-only.vie" | awk '{\
test_aln=$1;ref=$1 ;\
gsub("_test-only.vie", "_ref.vie", ref);\
gsub("_test-only.vie", "_testaln.fa", test_aln);\
printf "cat %s %s > tmp.vie\n" ,ref, $1;\
printf "kalign tmp.vie --reformat --rename -f fasta -o %s\n", test_aln }' > homfam_reformat.sh
find ~/kalignbenchmark/data/homfam -name "*_ref.vie" | awk '{ref=$1;gsub("_ref.vie", "_ref.msf", ref);printf "kalign %s --reformat --rename -f msf -o %s\n", $1,ref}' >> homfam_reformat.sh
chmod 755 homfam_reformat.sh
./homfam_reformat.shAlignment programs
export PATH=$HOME/kalignbenchmark/programs:$PATH
CPU=1
MEM=8
FMT=
IN=
OUT=
PROG=
function usage()
{
printf "usage: $0 -p <prog> -i <in> -o <out> \n\n" ;
printf "Options:\n-f <format>\n-t <threads>\n-m <mem>\n\n";
printf "Valid options for <prog> include:\n kalign\n kalign2\n muscle\n clustal\n\n";
exit 1;
}
while getopts t:m:p:i:o:f: opt
do
case ${opt} in
t) CPU=${OPTARG};;
m) MEM=${OPTARG};;
p) PROG=${OPTARG};;
i) IN=${OPTARG};;
o) OUT=${OPTARG};;
f) FMT=${OPTARG};;
*) usage;;
esac
done
if [ "${PROG}" == "" ]; then usage; fi
if [ "${IN}" == "" ]; then usage; fi
if [ "${OUT}" == "" ]; then usage; fi
SLURMMEM=$MEM"G"
CMD=
if [ "${PROG}" == "kalign2" ]; then
if [ "${FMT}" == "msf" ]; then
CMD="kalign2 -i $IN -f msf -o $OUT"
else
CMD="kalign2 -i $IN -o $OUT"
fi
fi
if [ "${PROG}" == "kalign" ]; then
if [ "${FMT}" == "msf" ]; then
CMD="kalign -i $IN -f msf -o $OUT"
else
CMD="kalign -i $IN -o $OUT"
fi
fi
if [ "${PROG}" == "muscle" ]; then
if [ "${FMT}" == "msf" ]; then
CMD="muscle3.8.31_i86linux32 -msf -in $IN -out $OUT"
else
CMD="muscle3.8.31_i86linux32 -in $IN -out $OUT"
fi
fi
if [ "${PROG}" == "clustal" ]; then
if [ "${FMT}" == "msf" ]; then
CMD="clustalo-1.2.4-Ubuntu-x86_64 --outfmt=msf --in $IN --out $OUT"
else
CMD="clustalo-1.2.4-Ubuntu-x86_64 --outfmt=a2m --in $IN --out $OUT"
fi
fi
HAS_SLURM=0
# printf "Running Sanity checks:\n";
if which sbatch >/dev/null; then
HAS_SLURM=1
fi
# echo $HAS_SLURM
if [ $HAS_SLURM = 1 ]; then
echo "YES"
sbatch <<EOT
#!/usr/bin/env bash
#SBATCH --cpus-per-task=$CPU
#SBATCH --mem=$SLURMMEM
#SBATCH -t 10-12:30 # time (D-HH:MM)
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
$CMD
exit 0
EOT
else
$CMD
fi
Time and score alignment (used in the homfam test)
export PATH=$HOME/kalignbenchmark/programs:$PATH
CPU=1
MEM=16
FMT=
IN=
OUT=
PROG=
function usage()
{
printf "usage: $0 -p <prog> -i <test aln> -r <ref aln> \n\n" ;
printf "Options:\n-f <format>\n-t <threads>\n-m <mem>\n\n";
printf "Valid options for <prog> include:\n kalign\n kalign2\n muscle\n clustal\n\n";
exit 1;
}
while getopts t:m:p:i:r: opt
do
case ${opt} in
t) CPU=${OPTARG};;
m) MEM=${OPTARG};;
p) PROG=${OPTARG};;
i) IN=${OPTARG};;
r) OUT=${OPTARG};;
*) usage;;
esac
done
if [ "${PROG}" == "" ]; then usage; fi
if [ "${IN}" == "" ]; then usage; fi
if [ "${OUT}" == "" ]; then usage; fi
SLURMMEM=$MEM"G"
CMD=
CMD="timescorealn -test $IN -ref $OUT -program $PROG --scratch $HOME/kalignbenchmark/scratch -out scores_homfam.csv"
HAS_SLURM=0
# printf "Running Sanity checks:\n";
if which sbatch >/dev/null; then
HAS_SLURM=1
fi
# echo $HAS_SLURM
if [ $HAS_SLURM = 1 ]; then
echo "YES"
sbatch <<EOT
#!/usr/bin/env bash
#SBATCH --cpus-per-task=$CPU
#SBATCH --mem=$SLURMMEM
#SBATCH -t 10-12:30 # time (D-HH:MM)
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
$CMD
exit 0
EOT
else
$CMD
fi
Place run script in bin of the benchmark directory .
cp run_aln.sh $HOME/kalignbenchmark/programs/
cp run_timealn.sh $HOME/kalignbenchmark/programs/SCRATCHDIR="~/kalignbenchmark/scratch"<<scratchdir>>DIR=`pwd`
function usage()
{
printf "This script will generate scripts to run kalign, clustal omega and muscle on the balibase MSA benchmark data set.\n\n" ;
printf "usage: $0\n\n" ;
exit 1;
}
while getopts h opt
do
case ${opt} in
h) usage;;
*) usage;;
esac
done
printf "Generating balibase run commands\n";
find ~/kalignbenchmark/data/bb3_release -name "*.tfa" |\
awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/);\
printf "run_aln.sh -p kalign -i %s -f msf -o %s/%s_%s_kalign.msf\n", $1,outdir,a[n-2],a[n-1];\
printf "run_aln.sh -p kalign2 -i %s -f msf -o %s/%s_%s_kalign2.msf\n", $1,outdir,a[n-2],a[n-1];\
printf "run_aln.sh -p muscle -i %s -f msf -o %s/%s_%s_muscle.msf\n", $1,outdir,a[n-2],a[n-1];\
printf "run_aln.sh -p clustal -i %s -f msf -o %s/%s_%s_clustal.msf\n", $1,outdir,a[n-2],a[n-1];\
}' > run_benchmark.sh
printf "Generating bralibase run commands\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*_test.fa" |\
grep unaligned |\
awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/);\
printf "run_aln.sh -p kalign -i %s -f msf -o %s/%s_%s_%s_kalign.msf\n", $1,outdir,a[n-4],a[n-3],a[n-2];\
printf "run_aln.sh -p kalign2 -i %s -f msf -o %s/%s_%s_%s_kalign2.msf\n", $1,outdir,a[n-4],a[n-3],a[n-2];\
printf "run_aln.sh -p muscle -i %s -f msf -o %s/%s_%s_%s_muscle.msf\n", $1,outdir,a[n-4],a[n-3],a[n-2];\
printf "run_aln.sh -p clustal -i %s -f msf -o %s/%s_%s_%s_clustal.msf\n", $1,outdir,a[n-4],a[n-3],a[n-2];\
}' >> run_benchmark.sh
printf "Generating Quantest2 run commands\n";
find ~/kalignbenchmark/data/QuanTest2/Test -name "*.vie" |\
awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/);\
printf "run_aln.sh -p kalign -i %s -o %s/%s_kalign.afa\n", $1,outdir,a[n-1];\
printf "run_aln.sh -p kalign2 -i %s -o %s/%s_kalign2.afa\n", $1,outdir,a[n-1];\
printf "run_aln.sh -p muscle -i %s -o %s/%s_muscle.afa\n", $1,outdir,a[n-1];\
printf "run_aln.sh -p clustal -i %s -o %s/%s_clustal.afa\n", $1,outdir,a[n-1];\
}' >> run_benchmark.sh
chmod 755 run_benchmark.shHere is the script to run the homfam test:
<<scratchdir>>DIR=`pwd`
function usage()
{
printf "This script will generate scripts to run kalign, clustal omega and muscle on the balibase MSA benchmark data set.\n\n" ;
printf "usage: $0\n\n" ;
exit 1;
}
while getopts h opt
do
case ${opt} in
h) usage;;
*) usage;;
esac
done
printf "export PATH=~/kalignbenchmark/programs:$PATH\n\n" > run_homfam.sh
find ~/kalignbenchmark/data/homfam -name "*_testaln.fa" | awk -v outdir="$SCRATCHDIR" '{
ref_aln=$1;gsub("_testaln.fa", "_ref.msf",ref_aln);
printf "run_timealn.sh -p kalign -i %s -r %s\n", $1,ref_aln;
printf "run_timealn.sh -p muscle -i %s -r %s\n", $1,ref_aln;
printf "run_timealn.sh -p clustal -i %s -r %s\n", $1,ref_aln;
}' >> run_homfam.sh
<<scratchdir>>printf "Generating kalign scoring run script\n";
find ~/kalignbenchmark/data/bb3_release -name "*.xml" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_kalign.msf | grep auto\n", $1,outdir,a[n-2],a[n-1] }' > score_bb3_kalign.sh
chmod 755 score_bb3_kalign.sh
find ~/kalignbenchmark/data/bb3_release -name "*.xml" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_kalign2.msf | grep auto\n", $1,outdir,a[n-2],a[n-1] }' > score_bb3_kalign2.sh
chmod 755 score_bb3_kalign2.sh
printf "Generating muscle scoring run script\n";
find ~/kalignbenchmark/data/bb3_release -name "*.xml" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_muscle.msf | grep auto\n", $1,outdir,a[n-2],a[n-1] }' > score_bb3_muscle.sh
chmod 755 score_bb3_muscle.sh
printf "Generating clustal scoring run script\n";
find ~/kalignbenchmark/data/bb3_release -name "*.xml" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_clustal.msf | grep auto\n", $1,outdir,a[n-2],a[n-1] }' > score_bb3_clustal.sh
chmod 755 score_bb3_clustal.sh
./score_bb3_kalign.sh > scores_balibase_kalign.csv
./score_bb3_kalign2.sh > scores_balibase_kalign2.csv
./score_bb3_muscle.sh > scores_balibase_muscle.csv
./score_bb3_clustal.sh > scores_balibase_clustal.csv
To plot the scores:
<<Rlibraries>>
readBaliscores <-function(file,name){
mat <- read.table(file);
colnames(mat) <- c("Type","Name","SP","TC")
mat$Type <- name
mat$Name <- sub(".*/" ,"", mat$Name)
mat$Name <- sub("[A-Z,_]*[.]{1}[A-Z]*$" ,"", mat$Name,ignore.case = TRUE)
mat <- as.tibble(mat)
x = str_split(mat$Name, "_", n = Inf, simplify = TRUE)
mat$Group <- x[,1]
return(mat)
}
The actual plotting:
library(ggplot2)
mat <- readBaliscores("scores_balibase_kalign.csv","kalign3");
mat <- rbind(mat,readBaliscores("scores_balibase_kalign2.csv","kalign2"));
mat <- rbind(mat,readBaliscores("scores_balibase_muscle.csv","muscle"));
mat <- rbind(mat,readBaliscores("scores_balibase_clustal.csv","clustalo"));
p <- ggplot(mat, aes(Group, SP))
p <- p + geom_boxplot(aes(colour = Type))
p <- p + scale_color_discrete(name = "Program")
p <- p + theme(legend.position = c(0.6, 0.15),legend.text=element_text(size=14),legend.direction = "horizontal")
p <- p + xlab(label="")
p <- p + ggtitle("Balibase benchmark")
p
# ggsave("Balibase_scores.jpeg",p,width = 18, height = 12, dpi = 300, units = c( "cm"))
## p1 <- p1 + geom_signif(comparisons = my_comparisons ,map_signif_level=TRUE)<<scratchdir>>printf "Generating kalign scoring run script\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.msf" | grep structural | awk -v outdir="$SCRATCHDIR" '{name=$1; gsub(/structural/, "unaligned"); n=split ($1,a,/[\/,.]/); printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_%s_kalign.msf | grep auto\n", name,outdir,a[n-4],a[n-3],a[n-2] }' > score_bralibase_kalign.sh
chmod 755 score_bralibase_kalign.sh
printf "Generating kalign2 scoring run script\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.msf" | grep structural | awk -v outdir="$SCRATCHDIR" '{name=$1; gsub(/structural/, "unaligned"); n=split ($1,a,/[\/,.]/); printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_%s_kalign2.msf | grep auto\n", name,outdir,a[n-4],a[n-3],a[n-2] }' > score_bralibase_kalign2.sh
chmod 755 score_bralibase_kalign2.sh
printf "Generating muscle scoring run script\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.msf" | grep structural | awk -v outdir="$SCRATCHDIR" '{name=$1; gsub(/structural/, "unaligned"); n=split ($1,a,/[\/,.]/); printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_%s_muscle.msf | grep auto\n", name,outdir,a[n-4],a[n-3],a[n-2] }' > score_bralibase_muscle.sh
chmod 755 score_bralibase_muscle.sh
printf "Generating clustalo scoring run script\n";
find ~/kalignbenchmark/data/data-set1 ~/kalignbenchmark/data/data-set2 -name "*.msf" | grep structural | awk -v outdir="$SCRATCHDIR" '{name=$1; gsub(/structural/, "unaligned"); n=split ($1,a,/[\/,.]/); printf "~/kalignbenchmark/programs/bali_score %s %s/%s_%s_%s_clustal.msf | grep auto\n", name,outdir,a[n-4],a[n-3],a[n-2] }' > score_bralibase_clustal.sh
chmod 755 score_bralibase_clustal.sh
./score_bralibase_kalign.sh > scores_bralibase_kalign.csv
./score_bralibase_kalign2.sh > scores_bralibase_kalign2.csv
./score_bralibase_muscle.sh > scores_bralibase_muscle.csv
./score_bralibase_clustal.sh > scores_bralibase_clustal.csvPlot scores
<<Rplotheader>>
library(ggplot2)
mat <- readBaliscores("scores_bralibase_kalign.csv","kalign3");
mat <- rbind(mat,readBaliscores("scores_bralibase_kalign2.csv","kalign2"));
mat <- rbind(mat,readBaliscores("scores_bralibase_muscle.csv","muscle"));
mat <- rbind(mat,readBaliscores("scores_bralibase_clustal.csv","clustalo"));
p <- ggplot(mat, aes(Group, SP))
p <- p + geom_boxplot(aes(colour = Type))
p <- p + scale_color_discrete(name = "Program")
p <- p + theme(legend.position = c(0.6, 0.15),legend.text=element_text(size=14),legend.direction = "horizontal")
p <- p + xlab(label="")
p <- p + ggtitle("Bralibase benchmark")
ggsave("Bralibase_scores.jpeg",p,width = 18, height = 12, dpi = 300, units = c( "cm"))
q
<<scratchdir>>printf "Generating kalign scoring run script\n";
find ~/kalignbenchmark/data/QuanTest2/Test -name "*.vie" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/data/QuanTest2/quantest2.py test@test %s/%s_kalign.afa ~/kalignbenchmark/data/QuanTest2/SS/%s.ss | grep kalignbenchmark \n", outdir,a[n-1],a[n-1] }' > score_quantest2_kalign.sh
chmod 755 score_quantest2_kalign.sh
printf "Generating kalign scoring run script\n";
find ~/kalignbenchmark/data/QuanTest2/Test -name "*.vie" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/data/QuanTest2/quantest2.py test@test %s/%s_kalign2.afa ~/kalignbenchmark/data/QuanTest2/SS/%s.ss | grep kalignbenchmark \n", outdir,a[n-1],a[n-1] }' > score_quantest2_kalign2.sh
chmod 755 score_quantest2_kalign2.sh
printf "Generating muscle scoring run script\n";
find ~/kalignbenchmark/data/QuanTest2/Test -name "*.vie" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/data/QuanTest2/quantest2.py test@test %s/%s_muscle.afa ~/kalignbenchmark/data/QuanTest2/SS/%s.ss | grep kalignbenchmark \n", outdir,a[n-1],a[n-1] }' > score_quantest2_muscle.sh
chmod 755 score_quantest2_muscle.sh
printf "Generating clustalo scoring run script\n";
find ~/kalignbenchmark/data/QuanTest2/Test -name "*.vie" | awk -v outdir="$SCRATCHDIR" '{n=split ($1,a,/[\/,.]/); ;printf "~/kalignbenchmark/data/QuanTest2/quantest2.py test@test %s/%s_clustal.afa ~/kalignbenchmark/data/QuanTest2/SS/%s.ss | grep kalignbenchmark \n", outdir,a[n-1],a[n-1] }' > score_quantest2_clustal.sh
chmod 755 score_quantest2_clustal.sh
./score_quantest2_kalign.sh > scores_quantest2_kalign.csv
./score_quantest2_kalign2.sh > scores_quantest2_kalign2.csv
./score_quantest2_muscle.sh > scores_quantest2_muscle.csv
./score_quantest2_clustal.sh > scores_quantest2_clustal.csv<<Rlibraries>>
readquanttestscores <-function(file,name){
mat <- read.table(file);
colnames(mat) <- c("Name","Score")
mat$Type <- name
mat$Name <- sub(".*/" ,"", mat$Name)
mat$Name <- sub("[_]{1}[A-Z]*[.]{1}[A-Z]*$" ,"", mat$Name,ignore.case = TRUE)
mat <- as_tibble(mat)
return(mat)
}
library(ggplot2)
mat <- readquanttestscores("scores_quanttest_clustalo.csv","clustalo")
mat <- rbind(mat, readquanttestscores("scores_quanttest_kalign.csv","kalign3"));
mat <- rbind(mat, readquanttestscores("scores_quantest2_kalign2.csv","kalign2"));
mat <- rbind(mat, readquanttestscores("scores_quanttest_muscle.csv","muscle"));
#mat <- mat %>% mutate(Score = as.dbl(Score))
p4 <- ggplot(mat, aes(Type, Score))
p4 <- p4 + geom_boxplot(aes(colour = Type))
p4 <- p4 + ggtitle("Quantest2 benchmark")
ggsave("Quantest2_scores.jpeg",p4,width = 16, height = 12, dpi = 300, units = c( "cm"))
<<Rplotheader>>
library(ggplot2)
mat <- read.csv("scores_homfam.csv");
p <- ggplot(mat, aes(NUMSEQ,Time))
p <- p + geom_point(aes(colour = Program,size = AVGLEN))
p <- p + scale_x_continuous(trans = 'log10', breaks=c(100,3000,10000,100000) ,labels = scales::comma)
p <- p + scale_y_continuous(trans = 'log10',breaks=c(0.01, 0.1, 1 , 10,100,1000,10000),labels=scales::comma )
p <- p + xlab("Number of sequences")
p <- p + ylab("Time (s)")
p <- p + ggtitle("HomFam benchmark")
p
ggsave("Homfam_scores.jpeg",p,width = 18, height = 12, dpi = 300, units = c( "cm")) libraries <- c("tidyverse","ggplot2","stringi","cowplot")
Script to test if libraries are present.
<<liblist>>
Sys.info()["nodename"]
for(library in libraries)
{
f = is.element(library, installed.packages()[,1])
print(paste("Library",library, "is installed?", f))
if(!f)
{
message("Missing library:",library )
quit(status=1)
}
}
quit(status=0)./test_for_libraries.Rnodename "work" [1] "Library tidyverse is installed? TRUE" [1] "Library ggplot2 is installed? TRUE" [1] "Library stringi is installed? TRUE" [1] "Library cowplot is installed? TRUE"
install.packages(“tidyverse”) Code block to load the libraries in R code.
<<liblist>>
lapply(libraries, FUN = function(X) {
do.call("library", list(X))
})