covplot

usage: blobtools covplot  -i BLOBDB -c COV [--max FLOAT]
                                [--xlabel XLABEL] [--ylabel YLABEL]
                                [--lib COVLIB] [-o PREFIX] [-m]
                                [-p INT] [-l INT] [--cindex] [-n] [-s]
                                [-r RANK] [-x TAXRULE] [--label GROUPS...]
                                [--sort ORDER] [--sort_first LABELS]
                                [--hist HIST] [--notitle]
                                [--colours FILE] [--exclude FILE]
                                [--refcov FILE] [--catcolour FILE]
                                [--format FORMAT] [--noblobs] [--noreads] [--legend]
                                [--cumulative]
                                [-h|--help]

    Options:
        -h --help                   show this
        -i, --infile BLOBDB         BlobDB file
        -c, --cov COV               COV file to be used in y-axis

        --xlabel XLABEL             Label for x-axis
        --ylabel YLABEL             Label for y-axis
        --max FLOAT                 Maximum values for x/y-axis [default: 1e10]

        --lib COVLIB                Plot only certain covlib(s). Separated by ","
        --notitle                   Do not add filename as title to plot
        -p, --plotgroups INT        Number of (taxonomic) groups to plot, remaining
                                     groups are placed in 'other' [default: 7]
        -l, --length INT            Minimum sequence length considered for plotting [default: 100]
        --cindex                    Colour blobs by 'c index' [default: False]
        -n, --nohit                 Hide sequences without taxonomic annotation [default: False]
        -s, --noscale               Do not scale sequences by length [default: False]
        --legend                    Plot legend of blobplot in separate figure
        -m, --multiplot             Multi-plot. Print blobplot for each (taxonomic) group separately
        --cumulative                Print plot after addition of each (taxonomic) group
        --sort <ORDER>              Sort order for plotting [default: span]
                                     span  : plot with decreasing span
                                     count : plot with decreasing count
        --sort_first <L1,L2,...>    Labels that should always be plotted first, regardless of sort order
                                     ("no-hit,other,undef" is often a useful setting)
        --hist <HIST>               Data for histograms [default: span]
                                     span  : span-weighted histograms
                                     count : count histograms
        -r, --rank <RANK>           Taxonomic rank used for colouring of blobs [default: phylum]
                                     (Supported: species, genus, family, order,
                                        phylum, superkingdom)
        -x, --taxrule <TAXRULE>     Taxrule which has been used for computing taxonomy
                                     (Supported: bestsum, bestsumorder) [default: bestsum]
        --format FORMAT             Figure format for plot (png, pdf, eps, jpeg,
                                        ps, svg, svgz, tiff) [default: png]
        --noblobs                   Omit blobplot [default: False]
        --noreads                   Omit plot of reads mapping [default: False]
        -o, --out PREFIX            Output prefix
        --label GROUPS...           Relabel (taxonomic) groups, can be used several times.
                                     e.g. "A=Actinobacteria,Proteobacteria"
        --colours COLOURFILE        File containing colours for (taxonomic) groups
        --exclude GROUPS            Exclude these (taxonomic) groups (also works for 'other')
                                     e.g. "Actinobacteria,Proteobacteria,other"
        --refcov <FILE>               File containing number of "total" and "mapped" reads
                                     per coverage file. (e.g.: bam0,900,100). If provided, info
                                     will be used in read coverage plot(s).
        --catcolour <FILE>            Colour plot based on categories from FILE
                                     (format : "seq,category").