blobtk plot

Command line

blobtk plot -h

Process a BlobDir and produce static plots. Called as `blobtk plot`

Usage: blobtk plot [OPTIONS] --blobdir <BLOBDIR>

Options:
  -d, --blobdir <BLOBDIR>
          Path to BlobDir directory
  -v, --view <VIEW>
          View to plot [possible values: blob, cumulative, legend, snail]
  -o, --output <OUTPUT>
          Output filename [default: output.svg]
  -f, --filter <FILTER>

  -s, --segments <SEGMENTS>
          Segment count for snail plot [default: 1000]
      --max-span <MAX_SPAN>
          Max span for snail plot
      --max-scaffold <MAX_SCAFFOLD>
          max scaffold length for snail plot
  -x, --x-field <X_FIELD>
          X-axis field for blob plot
  -y, --y-field <Y_FIELD>
          Y-axis field for blob plot
  -z, --z-field <Z_FIELD>
          Z-axis field for blob plot
  -c, --category <CAT_FIELD>
          Category field for blob plot
      --resolution <RESOLUTION>
          Resolution for blob plot [default: 30]
      --hist-height <HIST_HEIGHT>
          Maximum histogram height for blob plot
      --reducer-function <REDUCER_FUNCTION>
          Reducer function for blob plot [default: sum] [possible values: sum, max, min, count, mean]
      --scale-function <SCALE_FUNCTION>
          Scale function for blob plot [default: sqrt] [possible values: linear, sqrt, log]
      --scale-factor <SCALE_FACTOR>
          Scale factor for blob plot (0.2 - 5.0) [default: 1]
      --x-limit <X_LIMIT>
          X-axis limits for blob/cumulative plot (<min>,<max>)
      --y-limit <Y_LIMIT>
          Y-axis limits for blob/cumulative plot (<min>,<max>)
      --cat-count <CAT_COUNT>
          Maximum number of categories for blob/cumulative plot [default: 10]
      --legend <SHOW_LEGEND>
          Maximum number of categories for blob/cumulative plot [default: default] [possible values: default, full, compact, none]
      --cat-order <CAT_ORDER>
          Category order for blob/cumulative plot (<cat1>,<cat2>,...)
      --origin <ORIGIN>
          Origin for category lines in cumulative plot [possible values: o, x, y]
      --palette <PALETTE>
          Colour palette for categories [possible values: default, inverse, viridis]
      --color <COLOR>
          Individual colours to modify palette (<index>=<hexcode>)
  -h, --help
          Print help

Examples

Blob plot

blobtk plot -v blob -d /path/to/BlobDir -o blob_plot_filename.png

Cumulative plot

blobtk plot -v cumulative -d /path/to/BlobDir -o cumulative_plot_filename.png

Snail plot (SVG)

Output format (PNG or SVG) is determined by the output file suffix.

blobtk plot -v snail -d /path/to/BlobDir -o snail_plot_filename.svg

Legend only

blobtk plot -v legend -d /path/to/BlobDir -o legend_filename.png

Custom colours

The default palette is the 12 class paired colour scheme from colorbrewer2.org. The palette can be changed to an alternate pre-defined set of colours using the --palette option. Custom palettes may be defined by overriding one or more hex codes at specific indices (0 to n-1) using the --color option (which is applied after --palette). The palette may be extended beyond 12 colours by setting --cat-count and specifying additional hex codes.

blobtk plot ... --palette viridis --cat-count 14 --color 12=ff7001 --color 13=01ffff