Plot
cphasing plot -h
Usage: cphasing plot [OPTIONS]
Adjust or Plot the contacts matrix after assembling.
▌ Usage:
▌ • adjust the matrix by agp and plot a heatmap
cphasing plot -a groups.agp -m sample.10000.cool -o groups.500k.wg.png
▌ • adjust the matrix by agp and plot a 100k resolution heatmap
cphasing plot -a groups.agp \
-m sample.10000.cool \
-o groups.100k.wg.png \
-bs 100k
▌ • only plot a heatmap
cphasing plot -m sample.100k.cool -o sample.100k.png
▌ • Plot some chromosomes
cphasing plot -m sample.100k.cool -c Chr01,Chr02 -o Chr01_Chr02.100k.png
╭─ Options of Matrix Operation ────────────────────────────────────────────────╮
│ * --matrix -m Contacts matrix stored by Cool format. │
│ (COOL) │
│ [required] │
│ --binsize -bs Bin size of the heatmap you want to plot. Enabled │
│ suffix with k or m. [defalt: input matrix binsize] │
│ (STR) │
│ --only-coarsen Only coarsen the input matrix, do not need plot the │
│ heatmap. │
│ --balance balance the matrix. │
│ --balanced Plot balanced values, which need cool have weights │
│ columns in bins. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options of AGP Adjustment ──────────────────────────────────────────────────╮
│ --agp -a (AGP) │
│ --only-adjust Only adjust the matrix by agp, do not need plot the │
│ heatmap. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options of Heatmap ─────────────────────────────────────────────────────────╮
│ --chromosomes -c Chromosomes and order in which │
│ the chromosomes should be │
│ plotted. Comma seperated. or a │
│ one column file │
│ (TEXT) │
│ --disable-natural-sort -dns Disable natural sort of │
│ chromosomes, only used for │
│ --chromosomes or --only-chr │
│ --per-chromosomes,--per-chromos… -pc Instead of plotting the whole │
│ matrix, each chromosome is │
│ plotted next to the other. │
│ --only-chr -oc Only plot the chromosomes that │
│ ignore unanchored contigs. When │
│ --chromosomes specifed, this │
│ parameter will be ignored. The │
│ default use prefix of Chr to │
│ find the chromosomes. │
│ --chr-prefix can be used to │
│ change this. │
│ --chr-prefix -cp Prefix of the chromosomes, only │
│ used for --only-chr │
│ (STR) │
│ [default: Chr] │
│ --chrom-per-row -cpr Number of chromosome plot in │
│ each row │
│ (INTEGER) │
│ [default: 4] │
│ --vmin -vmin (FLOAT) │
│ --vmax -vmax (FLOAT) │
│ --scale -s Method of contact normalization │
│ (STR) │
│ [default: log1p] │
│ --triangle Plot the heatmap in triangle │
│ --fontsize Fontsize of the ticks, default │
│ is auto │
│ (INT) │
│ --dpi -dpi Resolution for the image. │
│ (INTEGER) │
│ [default: 600] │
│ --cmap,--colormap -cmap,-cm Colormap of heatmap. Available │
│ values can be seen : │
│ https://pratiman-91.github.io/… │
│ and │
│ http://matplotlib.org/examples… │
│ and whitered . │
│ (TEXT) │
│ [default: redp1_r] │
│ --no-lines -nl Don't add dash line in │
│ chromosome boundaries. │
│ --no-ticks -nt Don't add ticks both in x axis │
│ and y axis. │
│ --rotate-xticks -rx Rotate the x ticks │
│ [default: True] │
│ --rotate-yticks -ry Rotate the x ticks │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Global Options ─────────────────────────────────────────────────────────────╮
│ --output -o Output path of file. │
│ (TEXT) │
│ [default: plot.heatmap.png] │
│ --threads -t Number of threads. (unused) │
│ (INT) │
│ [default: 4] │
│ --help -help,-h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
Examples#
Plot from .agp and contig-level .cool#
Note
This function will generate two intermedia sample.10000.chrom.cool and sample.500k.chrom.cool.