External Control of Gitools

As of version 1.7.0 Gitools can be addressed from outside of the application. At the moment there is one command availabe.

Gitools is listening to the port 50151 by default. So it is possible to send the commands to this port. Alternatively it is possible to change the port by editing the ui.xml file in the Gitools configuration folder. (For Linux and Mac OS X users this should be at /.gitools).

Overview of commands

Command Description Options as of Version
add-header-colored-labels Adds a new colored labels header
  • -c (--color) <color> : A Hex color as ‘#FF0000’ - depends on –value
  • -n (--no-auto-generate) : Specify if auto color generation is not desired.
  • -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
  • -d (--dimension) <dim> : Indicate where to add the header: ‘rows’ or ‘columns’.
  • -t (--text-visible) : Set for visible text labels
  • -v (--value) <value> : A value corresponding to a color
  • -h (--heatmap) <heatmap> : (Optional) Heatmap name or last for the last added
2.0.0
add-header-text-labels Adds a new text header to the heatmap
  • -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
  • -d (--dimension) <dim> : Indicate where to add the header: ‘rows’ or ‘columns’.
  • -h (--heatmap) <heatmap> : Heatmap name. Not compulsory if one is open.
2.0.0
close Closes a heatmap and optionally saves (as)
  • -a (--as) <FILE_NAME> : path and filename indicating where to save the heatmap
  • -d (--discard-hidden) : Discard hidden data
  • -h (--heatmap) <heatmap> : (optional) ‘LAST’ or heatmap name
  • -o (--optimize) : Optimize data file (slower saving process)
  • -s (--save) : Save current state as heatmap
2.2.1
help Prints all available commands    
load matrix-file Tells Gitools to load a file.
  • --rows** (-r) : File rows annotations
  • --cols (-c) : File cols annotations
1.7.0
sort-by-annotation Sorts the heatmap by col or row annotation
  • -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
  • -d (--dimension) <dim> : Indicate where to add the header: ‘rows’ or ‘columns’.
  • -h (--heatmap) <heatmap> : Heatmap name. Not compulsory if one is open.
2.2.0
sort-mutex Sorts the visible layer by mutual excl.
  • -d (--dimension) <dimension> : Indicate where to add the header: ‘rows’ or ‘columns’.
  • -h (--heatmap) <heatmap> : (optional) ‘LAST’ or heatmap name
  • -i (--identifier) <identifier> : Specify this option for each identifier which you want to include in the mutex sorting
  • -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
  • -s (--sort) <sort> : Sort according to header. Specify either asc[ending] or desc[ending].
2.2.1
version Prints Gitools version.   1.7.1

How to send a command to Gitols

There is several ways to send the commands listed above to Gitools. We will make three examples here:

Command line

With a terminal application that lets you execute command line you can create a new Gitools instance with command to execute upon startup.

gitools load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv

HTTP

By HTTP it is possible to send the command like this:

http://localhost:50151/load?file=/home/user/matrix-file.tdm&cols=/home/user/col-annotations.tsv&rows=/home/user/row-annotations.tsv

Python

Python or any other programming environment can make use of the  Telnet internet protocol. See below to understand how python can connect to Gitools and send it a command.

import socket
def gitools_command(command):
    gitools = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
    gitools.connect(("localhost", 50151))
    gitools.sendall( command.encode('utf-8'))
    gitools.close()

command = "load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv"
gitools_command(command)

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