PlotMeth

BatMeth2: An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

python library

install library required

pip install numpy
pip install pandas
pip install matplotlib
pip install seaborn

bt2profile

Plot DNA methlation profile across gene/ TE/ predefined bed region, such as peak or dmr region. The input DNA methylation level matrix is produced by Calulate mC across predefined regions.

The *.TSSprofile.txt *.centerprofile.txt and *.AverMethylevel.txt are calulated by Calulate mC across predefined regions.

$ BatMeth2 methyGff -o H3K4me3.bdgene H3K4me3.unbdgene \
    -G genome.fa -m methratio.txt \
    -b H3K4me3.bdgene.bed H3K4me3.unbdgene.bed -B

$ bt2profile.py -f H3K4me3.bdgene.TSSprofile.txt \
    H3K4me3.unbdgene.TSSprofile.txt \
    -l H3K4me3.bdgene H3K4me3.unbdgene \
    --outFileName H3K4me3.output.meth.pdf \
    -s 1 1 -xl up2k TSS down2k --context C

$ BatMeth2 methyGff -o active random \
    -G genome.fa -m methratio.txt \
    -b active.bed random.bed -B

$ bt2profile.py -f active.centerprofile.txt \
    random.centerprofile.txt \
    -l active random \
    --outFileName active_random.output.meth.pdf \
    -s 1 1 -xl up2k center down2k

$ bt2profile.py -f H3K27me3.bdgene.AverMethylevel.txt \
    H3K27me3.unbdgene.AverMethylevel.txt \
    -l H3K27me3.bdgene H3K27me3.unbdgene \
    --outFileName H3K27me3.output.meth.pdf \
    -s 1 1 1 -xl up2k TSS TES down2k

bt2basicplot

$ python3 bt2basicplot.py -c coverfile.txt coverfile2.txt -o tt.pdf

$ python3 bt2basicplot.py -f prefix1.gene.cg.txt prefix2.gene.cg.txt \
    -c coverfile.txt coverfile2.txt -o tt.pdf

bt2chrprofile

bt2heatmap

$ python bt2heatmap.py -m H3K4me3.bdgene.GENE.cg.txt -l bg \
-o test0.pdf -z k43 -sl TSS -el TTS

$ python bt2heatmap.py -m H3K4me3.bdgene.TSS.cg.txt H3K4me3.bdgene.TTS.cg.txt \
    -l tss tts -o test.pdf --zMax 0.1 --colorMap vlag --centerlabel center -z bd

$ python bt2heatmap.py -m H3K4me3.bdgene.TSS.cg.txt H3K4me3.bdgene.TTS.cg.txt \
    H3K4me3.unbdgene.TSS.cg.txt H3K4me3.unbdgene.TTS.cg.txt \
    -l test end -o test2.pdf --zMax 0.05 --centerlabel center \
    --plotmatrix 2x2 --colorList white,red -z bd unbd

$ python bt2heatmap.py -f H3K4me3.bdgene.body.cg.txt H3K4me3.bdgene.body.cg.txt \
    H3K4me3.unbdgene.body.cg.txt H3K4me3.unbdgene.body.cg.txt \
    -l test end -o test3.pdf --zMax 0.5 --centerlabel center \
    --plotmatrix 2x2 -z bd unbd

$ python bt2heatmap.py -m H3K4me3.bdgene.TSS.cg.txt H3K4me3.bdgene.TTS.cg.txt \
    H3K4me3.bdgene.TSS.chg.txt H3K4me3.bdgene.TTS.chg.txt \
    H3K4me3.bdgene.TSS.chh.txt H3K4me3.bdgene.TTS.chh.txt \
    -l H3K4me3.bdgene-tss H3K4me3.bdgene-tts \
    -o H3K4me3.bdgene.TSS_TTS.heatmap.pdf --plotmatrix 3x2 \
    --centerlabel center -z cg chg chh --zMax 0.3 1 0.01

Tip

DNA methylation level distribution on chromosome (bt2chrplot) and DNA methylation level distribution (bt2visul) are currently being tested, and we will update them as soon as possible.

Note: @HZAU.

Tip

For feature requests or bug reports please open an issue on github.