matplot

Description

distmat produces several output files containing matrix data. matplot can be used to visualize these data as a 2D map plot.

Command summary

gmx_clusterByFeatures matplot [-h] [-i distmat.dat] [-o output.png]
                              [-xs 1] [-ys 1] [-xl Residue]
                              [-yl Residue] [-cbl nm] [-a auto]
                              [-cmap binary] [-vmin VMIN] [-vmax VMAX]
                              [-fs 14] [-cbor vertical] [-wd 8] [-ht 8]
                              [-dpi 300]

Options

-i distmat.dat, --input distmat.dat

Input file containing matrix-data. This file is obtained as a output from distmat.

-o output.png, --output output.png

Name of the output matrix-plot file. The extension will be used to determine the output format.

Following output formats (system dependent) might be available:
  • ps : Postscript
  • eps : Encapsulated Postscript
  • pdf : Portable Document Format
  • pgf : PGF code for LaTeX
  • png : Portable Network Graphics
  • raw : Raw RGBA bitmap
  • rgba : Raw RGBA bitmap
  • svg : Scalable Vector Graphics
  • svgz : Scalable Vector Graphics
  • jpg : Joint Photographic Experts Group
  • jpeg : Joint Photographic Experts Group
  • tif : Tagged Image File Format
  • tiff : Tagged Image File Format

Note

To list the output formats, use gmx_clusterByFeatures matplot -h.

-xs 1, --x-start 1

First residue number along X-axis. Input file does not contain information about residue number. Therefore, this option can be used to set the number of residues along X-axis.

-ys 1, --y-start 1

First residue number along Y-axis. Input file does not contain information about residue number. Therefore, this option can be used to set the number of residues along Y-axis.

-xl Residue, --x-label Residue

X-axis label

-yl Residue, --y-label Residue

Y-axis label

-cbl (nm), --colorbar-label (nm)

Label for color bar

-a auto, --image-aspect auto

Controls the aspect ratio of the axes. The aspect is of particular relevance for images since it may distort the image, i.e. pixel will not be square.

Following two options are available:
  • -a equal : Ensures an aspect ratio of 1. Pixels will be square.
  • -a auto : The axes is kept fixed and the aspect is adjusted so
    that the data fit in the axes. In general, this will result in non-square pixels.

-cmap binary, --colormap binary

Name of colormap by which matrix image will be colored. To preview the available colormaps, visit colormaps list.

Following colormaps might be available:

Accent           Blues            BrBG             BuGn
BuPu             CMRmap           Dark2            GnBu             Greens
Greys            OrRd             Oranges          PRGn             Paired
Pastel1          Pastel2          PiYG             PuBu             PuBuGn
PuOr             PuRd             Purples          RdBu             RdGy
RdPu             RdYlBu           RdYlGn           Reds             Set1
Set2             Set3             Spectral         Wistia           YlGn
YlGnBu           YlOrBr           YlOrRd           afmhot           autumn
binary           bone             brg              bwr              cividis
cool             coolwarm         copper           cubehelix        flag
gist_earth       gist_gray        gist_heat        gist_ncar        gist_rainbow
gist_stern       gist_yarg        gnuplot          gnuplot2         gray
hot              hsv              inferno          jet              magma
nipy_spectral    ocean            pink             plasma           prism
rainbow          seismic          spring           summer           tab10
tab20            tab20b           tab20c           terrain          viridis
winter

Reverse of the available colormaps are also available with same name suffixed by “_r”. For example, reverse of binary colormap is binary_r, reverse of gist_earth is gist_earth_r etc.

Note

To list all available colormaps, use gmx_clusterByFeatures matplot -h.

-vmin VMIN, --min-value VMIN

Minimum value to begin color-mapping. If not provided, minimum value of whole matrix will be considered.

-vmax VMAX, --max-value VMAX

Maximum value to end color-mapping. If not provided, maximum value of whole matrix will be considered.

-fs 14, --font-size 14

Font-size of all texts in plot

-cbor vertical, --colorbar-orientation vertical

Orientation of color bar Following keywords are available: * -cbor vertical - vertical colorbar at right side * -cbor horizontal - horizontal colorbar at top

-wd 8, --width 8

Width of plot in inch

-ht 8, --height 8

Height of plot in inch

-dpi 300, --dpi 300

Resolution of plot