Configuration file

Setting up your configuration file:

Here are some notes in order to have a well established configuration file to get your desired karyoplot.

Sections and Options:

A configuration file must have atleast 2 sections:

One entitled canvas and the other sequence, where they each have optional and mandatory options. A canvas section will contains the settings for the canvas of the whole cartoon and the sequence section allows you to get your data file and set the parameters for every chromosome in your genome.

canvas

Option	Description	Type	Requirements	Default
title	Title of the karyoplot	string	Optional	None
background_color	Sets the karyoplot’s background color	string	Optional	white
width	Sets the width dimension of the canvas	integer	Optional	10
height	Sets the height dimension of the canvas	integer	Optional	10
constrained_layout	Ensures the good layout of the final image	boolean	Optional	False
title_fontsize	Font size for the Canvas’ title	integer	Optional	20

sequence

Option	Description	Type	Requirements	Default
reference	FASTA file	.fasta or .fasta.gz	Mandatory	None
color	Chromosome color on the plot	string	Optional	black
limitesize	Minimum size for a chromosome to be shown in the karyoplot	integer	Optional	50
size	Size of the plot	integer	Optional	1
zoom	List of names of chromosomes followed by the positions for the zoom	string	Optional	None
scale	Shows each chromosome’s plot scale(sci notation)	boolean	Optional	False
seq_fontsize	Font size for the chromosomes’ titles	integer	Optional	14
x_label_fontsize	Font size for the chromosomes’ x labels	integer	Optional	20

We must precise that if the zoom option is specified the limitesize is no longer taken into account.

From this simple example you will obtain an image with your genome’s chromosomes.

To add features to your chromosomes, new sections must be added, therefore a track section is required for each feature. A feature’s section must always start by track_ and finish with anything but a space. Each track’s name must be unique.

track

Option	Description	Type	Requirements	Default
title	Title for the feature	string	Optional	None
color	Color for the feature	string	Optional	red
colorin	Use colors in the 5th column of bed file	boolean	Optional	False
size	Size of the feature’s plot	integer	Optional	1
data	BED file with the feature information	.bed.gz	Mandatory	None
datatype	The type of file input in Data	bed	Mandatory	None
thickness	The width of the feature’s plot	integer	Optional	1
background_color	The background color for the plot	string	Optional	white

Some feature may require additional functions such as calculating a percentage for instance. In that case, 3 new options are added to track to recognize those features.

Option	Description	Type	Requirements	Default
graph_type	The type of graph needed	gc	Mandatory	None
GC_window_length	Sliding window length	integer	Optional	1000
GC_window_overlap	Sliding window overlap length	integer	Optional	100
scaley	Shows the plot’s y axis scale(sci notation)	boolean	Optional	False
y_label_fontsize	Font size for the track’s y labels	integer	Optional	20

Note

In this current version only GC percentages can be obtained with the last track seen.

To get a better idea of how these configuration files work, take a look at the use_cases.