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