jvarkit

SimplePlot

Last commit

simple figure plotter output is a R script

Usage

Usage: simpleplot [options] Files
  Options:
    -chrompos, --chrom-position
      When reading a genomic file. Input is not a BED file but a CHROM(tab)POS 
      file. e.g: output of `samtools depth`
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --hide-legend
      Hide Legend
      Default: false
    --min-reference-size
      When using a *.dict file, discard the contigs having a length < 'size'. 
      Useful to discard the small unused contigs like 'chrM'. -1 : ignore.
      Default: -1
    -nh, --no-header
      There is no header. Tested for Histograms
      Default: false
    -o, --out
      Output file. If defined, save the picture in this file extension:png, 
      jpg or R (experimental) and close the application.
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    -su, --sort-unique
      For PIE or SIMPLE_HISTOGRAM the input is the output of a `sort | uniq 
      -c` pipeline
      Default: false
    --title
      Chart Title
      Default: <empty string>
    --type, -t
      type
      Default: UNDEFINED
      Possible Values: [UNDEFINED, BEDGRAPH, PIE, SIMPLE_HISTOGRAM, HISTOGRAM, STACKED_HISTOGRAM, STACKED_HISTOGRAM_PIVOTED, XYV, STACKED_XYV, HEATMAP]
    --version
      print version and exit
    -xlab, -xlabel, --xlabel
      X axis label.
    -ylab, -ylabel, --ylabel
      Y axis label.

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew simpleplot

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SimplePlot.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/SimplePlotTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite simpleplot ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Plot types:

Year X Y 2018 1 2 2019 3 4

Examples

$ gunzip -c in.vcf.gz | grep -v "^#" | cut -f 1 | sort | uniq -c | java -jar dist/simpleplot.jar -t SIMPLE_HISTOGRAM  -su 
$ gunzip -c in.vcf.gz | grep -v "^#" | cut -f 1 | sort | uniq -c | java -jar dist/simpleplot.jar -t PIE  -su

HISTOGRAM

Year  X  Y
2018  1  2
2019  3  4

$ echo -e "Year\tX\tY\n2018\t1\t2\n2019\t3\t4" | java -jar dist/simpleplot.jar -t HISTOGRAM

produces a histogram with two series in the legend (2018 and 2019). On the X-axis: 4 items X-2018, X-2019, Y-2018, Y-2019

STACKED_HISTOGRAM

Year  X  Y
2018  1  2
2019  3  4

$ echo -e "Year\tX\tY\n2018\t1\t2\n2019\t3\t4" | java -jar dist/simpleplot.jar -t STACKED_HISTOGRAM

produces a histogram with two series in the legend (2018 and 2019). On the X-axis: 2 items X( 2018 under-2019), Y (2018 under 2019)

STACKED_HISTOGRAM_PIVOTED

Year  X  Y
2018  1  2
2019  3  4

$  echo -e "2018\t1\t2\n2019\t3\t4\n2020\t1\t10" | java -jar dist/simpleplot.jar -t STACKED_HISTOGRAM_PIVOTED -nh

produces a histogram with two series in the legend ($1 and $2). On the X-axis: 3 items 2018, 2019, 2020. Each with the stacked $1 and $2

Example

plot base=function(position) in a fastq:

gunzip -c src/test/resources/S1.R1.fq.gz | \
	awk '(NR%4==2) {L=length($0);for(i=1;i<=L;i++) printf("%d\t%s\n",i,substr($0,i,1));}' |\
	sort | uniq -c |\
	java -jar dist/simpleplot.jar -su -t STACKED_XYV --xlabel "Position"

Example

HeatMap

echo -e "A\tA\t1\nA\tB\t2\nB\tA\t3\nB\tB\t10" | java -jar dist/simpleplot.jar  -t HEATMAP

History

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