Tool:trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files

Question

[poisonAlien]

If you are working with chip-seq or atac-seq or any assays resulting in bigWig files, one of the common visualizations is to generate track plots displaying signal intensities across genomic loci. Libraries in R like Gviz facilitates such visualization but they are slow, complicated, and come with a large number of dependencies, not to mention R versions themselves.

Introducing trackplot - a fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files in R. trackplot has only two depdencies namely data.table R package, and bwtool CLI tool.

Features:

• Its fast since most of the heavy lifting is done by bwtool
• Plots are generated using pure base graphics (no ggplot2 or tidyverse dependencies)
• Automatically queries UCSC genome browser for gene models.
• Supports GTF and standard UCSC gene formats as well.
• Customization: Each track can be customized for color, scale, height/width.
• Region highlighting, gene track collapsing, etc

Usage:

trackplot is a standalone R script and requires no installation. Just source it and you're good to go!

Source code on Github. Comments and suggestions are always welcome :)

# download and source the script  
> download.file(url = "https://raw.githubusercontent.com/PoisonAlien/trackplot/master/trackplot.R", destfile = "trackplot.R") 
> source('trackplot.R') 

> trackplot(bigWigs = c("CD34.bw", "EC.bw", "LC.bw", "CD4p.bw", "CD8p.bw"),   
          loci = "chr3:187,715,903-187,752,003",   
          draw_gene_track = TRUE, build = "hg38", mark_regions = markregions,   
          custom_names = c("CD34", "EC", "LC", "CD4+", "CD8+") )

edit: Answering the comments, bwtool pre-built binaries are now included as part of the trackplot repository. Just make them executable and start using them.

[Vishal]

Getting this error on MacOS 10.14.6

gcc -DHAVE_CONFIG_H -I. -I..    -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O0 -I/Users/kopardevn/SandBox/bwtool/libbeato/include -MT metaBigBam.o -MD -MP -MF .deps/metaBigBam.Tpo -c -o metaBigBam.o metaBigBam.c
metaBigBam.c:485:12: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead
      [-Wdeprecated-declarations]
    if (h->cigar_tab == 0)
           ^
/usr/local/include/htslib/sam.h:77:29: note: 'cigar_tab' has been explicitly marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
metaBigBam.c:487:5: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead
      [-Wdeprecated-declarations]
        h->cigar_tab = (int8_t*)calloc(128, sizeof(int8_t));
           ^
/usr/local/include/htslib/sam.h:77:29: note: 'cigar_tab' has been explicitly marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
metaBigBam.c:489:9: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead
      [-Wdeprecated-declarations]
            h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
               ^
/usr/local/include/htslib/sam.h:77:29: note: 'cigar_tab' has been explicitly marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
metaBigBam.c:489:42: error: read-only variable is not assignable
            h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
metaBigBam.c:502:35: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead
      [-Wdeprecated-declarations]
        op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
                                         ^
/usr/local/include/htslib/sam.h:77:29: note: 'cigar_tab' has been explicitly marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
4 warnings and 1 error generated.
make[2]: *** [metaBigBam.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any idea whats going on? Also seems like others are running into the same problem ( https://github.com/CRG-Barcelona/libbeato/issues/9 ). A solution will be appreciated.

[poisonAlien]

Try these instructions for bwtool compilation. It should work. Copied below as well.

git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'
git clone https://github.com/madler/zlib

cd libbeato/
git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2
./configure
make
cd ..

cd zlib
./configure
make
cd ..

cd bwtool/
./configure CFLAGS='-I../libbeato -I../zlib' LDFLAGS='-L../libbeato/jkweb -L../libbeato/beato -L../zlib'
make

# copy/move the binary to PATH or to a directory under PATH
sudo cp bwtool /usr/local/bin

[Sael]

Hi I tried your script to make the plots but got an error

Parsing loci..
Queried region: chr1:202717141-202817514 [100373 bps]
Checking for files..
 Error in .check_bwtool() : 
Could not locate bwtool. Download it from here: https://github.com/CRG-Barcelona/bwtool/releases

The bwtool installed using the same lines above.

git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'
git clone https://github.com/madler/zlib

cd libbeato/
git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2
./configure
make
cd ..

cd zlib
./configure
make
cd ..

cd bwtool/
./configure CFLAGS='-I../libbeato -I../zlib' LDFLAGS='-L../libbeato/jkweb -L../libbeato/beato -L../zlib'
make

R session

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 18.04.5 LTS

Matrix products: default

BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1

LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C



attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.2    parallel_3.6.2    tools_3.6.2       tinytex_0.27      data.table_1.13.2 xfun_0.19

[ATpoint]

Did you add it to PATH or to a folder in PATH?

[Sael]

I just added it to PATH. Still I get the same error.

[Sael]

Problem solved using:

git clone https://github.com/CRG-Barcelona/libbeato.git
git clone https://github.com/CRG-Barcelona/bwtool.git
cd libbeato/
./configure
git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2
make
sudo make install
cd ../bwtool/
./configure
make
sudo make install

[poisonAlien]

You are almost there. You just need to copy/move the binary to a PATH (e.g; /usr/local/bin) or to a directory under PATH.