{"__v":0,"_id":"5798a74717ced017003c4c78","category":{"__v":0,"_id":"57989a8817ced017003c4c69","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-07-27T11:27:04.750Z","from_sync":false,"order":3,"slug":"docstrings","title":"Documentation"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-07-27T12:21:27.957Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":3,"body":"[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"usage: blobtools covplot  -i BLOBDB -c COV [--max FLOAT]\\n                                [--xlabel XLABEL] [--ylabel YLABEL]\\n                                [--lib COVLIB] [-o PREFIX] [-m]\\n                                [-p INT] [-l INT] [--cindex] [-n] [-s]\\n                                [-r RANK] [-x TAXRULE] [--label GROUPS...]\\n                                [--sort ORDER] [--hist HIST] [--notitle]\\n                                [--colours FILE] [--exclude FILE]\\n                                [--refcov FILE] [--catcolour FILE]\\n                                [--format FORMAT] [--noblobs] [--noreads] [--legend]\\n                                [--cumulative]\\n                                [-h|--help]\\n\\n    Options:\\n        -h --help                   show this\\n        -i, --infile BLOBDB         BlobDB file\\n        -c, --cov COV               COV file to be used in y-axis\\n\\n        --xlabel XLABEL             Label for x-axis\\n        --ylabel YLABEL             Label for y-axis\\n        --max FLOAT                 Maximum values for x/y-axis [default: 1e10]\\n\\n        --lib COVLIB                Plot only certain covlib(s). Separated by \\\",\\\"\\n        --notitle                   Do not add filename as title to plot\\n        -p, --plotgroups INT        Number of (taxonomic) groups to plot, remaining\\n                                     groups are placed in 'other' [default: 7]\\n        -l, --length INT            Minimum sequence length considered for plotting [default: 100]\\n        --cindex                    Colour blobs by 'c index' [default: False]\\n        -n, --nohit                 Hide sequences without taxonomic annotation [default: False]\\n        -s, --noscale               Do not scale sequences by length [default: False]\\n        --legend                    Plot legend of blobplot in separate figure\\n        -m, --multiplot             Multi-plot. Print blobplot for each (taxonomic) group separately\\n        --cumulative                Print plot after addition of each (taxonomic) group\\n        --sort <ORDER>              Sort order for plotting [default: span]\\n                                     span  : plot with decreasing span\\n                                     count : plot with decreasing count\\n        --hist <HIST>               Data for histograms [default: span]\\n                                     span  : span-weighted histograms\\n                                     count : count histograms\\n        -r, --rank <RANK>           Taxonomic rank used for colouring of blobs [default: phylum]\\n                                     (Supported: species, genus, family, order,\\n                                        phylum, superkingdom)\\n        -x, --taxrule <TAXRULE>     Taxrule which has been used for computing taxonomy\\n                                     (Supported: bestsum, bestsumorder) [default: bestsum]\\n        --format FORMAT             Figure format for plot (png, pdf, eps, jpeg,\\n                                        ps, svg, svgz, tiff) [default: png]\\n        --noblobs                   Omit blobplot [default: False]\\n        --noreads                   Omit plot of reads mapping [default: False]\\n        -o, --out PREFIX            Output prefix\\n        --label GROUPS...           Relabel (taxonomic) groups, can be used several times.\\n                                     e.g. \\\"A=Actinobacteria,Proteobacteria\\\"\\n        --colours COLOURFILE        File containing colours for (taxonomic) groups\\n        --exclude GROUPS            Exclude these (taxonomic) groups (also works for 'other')\\n                                     e.g. \\\"Actinobacteria,Proteobacteria,other\\\"\\n        --refcov <FILE>               File containing number of \\\"total\\\" and \\\"mapped\\\" reads\\n                                     per coverage file. (e.g.: bam0,900,100). If provided, info\\n                                     will be used in read coverage plot(s).\\n        --catcolour <FILE>            Colour plot based on categories from FILE\\n                                     (format : \\\"seq,category\\\").\",\n      \"language\": \"text\"\n    }\n  ]\n}\n[/block]","excerpt":"","slug":"covplot-1","type":"basic","title":"covplot"}
[block:code] { "codes": [ { "code": "usage: blobtools covplot -i BLOBDB -c COV [--max FLOAT]\n [--xlabel XLABEL] [--ylabel YLABEL]\n [--lib COVLIB] [-o PREFIX] [-m]\n [-p INT] [-l INT] [--cindex] [-n] [-s]\n [-r RANK] [-x TAXRULE] [--label GROUPS...]\n [--sort ORDER] [--hist HIST] [--notitle]\n [--colours FILE] [--exclude FILE]\n [--refcov FILE] [--catcolour FILE]\n [--format FORMAT] [--noblobs] [--noreads] [--legend]\n [--cumulative]\n [-h|--help]\n\n Options:\n -h --help show this\n -i, --infile BLOBDB BlobDB file\n -c, --cov COV COV file to be used in y-axis\n\n --xlabel XLABEL Label for x-axis\n --ylabel YLABEL Label for y-axis\n --max FLOAT Maximum values for x/y-axis [default: 1e10]\n\n --lib COVLIB Plot only certain covlib(s). Separated by \",\"\n --notitle Do not add filename as title to plot\n -p, --plotgroups INT Number of (taxonomic) groups to plot, remaining\n groups are placed in 'other' [default: 7]\n -l, --length INT Minimum sequence length considered for plotting [default: 100]\n --cindex Colour blobs by 'c index' [default: False]\n -n, --nohit Hide sequences without taxonomic annotation [default: False]\n -s, --noscale Do not scale sequences by length [default: False]\n --legend Plot legend of blobplot in separate figure\n -m, --multiplot Multi-plot. Print blobplot for each (taxonomic) group separately\n --cumulative Print plot after addition of each (taxonomic) group\n --sort <ORDER> Sort order for plotting [default: span]\n span : plot with decreasing span\n count : plot with decreasing count\n --hist <HIST> Data for histograms [default: span]\n span : span-weighted histograms\n count : count histograms\n -r, --rank <RANK> Taxonomic rank used for colouring of blobs [default: phylum]\n (Supported: species, genus, family, order,\n phylum, superkingdom)\n -x, --taxrule <TAXRULE> Taxrule which has been used for computing taxonomy\n (Supported: bestsum, bestsumorder) [default: bestsum]\n --format FORMAT Figure format for plot (png, pdf, eps, jpeg,\n ps, svg, svgz, tiff) [default: png]\n --noblobs Omit blobplot [default: False]\n --noreads Omit plot of reads mapping [default: False]\n -o, --out PREFIX Output prefix\n --label GROUPS... Relabel (taxonomic) groups, can be used several times.\n e.g. \"A=Actinobacteria,Proteobacteria\"\n --colours COLOURFILE File containing colours for (taxonomic) groups\n --exclude GROUPS Exclude these (taxonomic) groups (also works for 'other')\n e.g. \"Actinobacteria,Proteobacteria,other\"\n --refcov <FILE> File containing number of \"total\" and \"mapped\" reads\n per coverage file. (e.g.: bam0,900,100). If provided, info\n will be used in read coverage plot(s).\n --catcolour <FILE> Colour plot based on categories from FILE\n (format : \"seq,category\").", "language": "text" } ] } [/block]