Use Cases

Using these 2 files [fasta] and [bed] , here are some concrete examples of how to use your configuration file to adjust your karyoplot to your convenience. We have the input configurations files followed by the output images.

A karyoplot with no features

With a zoom :

[canvas]
title = My Karyoplot
background_color = white
width = 30
height = 25
constrained_layout = True
title_fontsize = 30

[sequence]
reference = $HOME/user/chromosome.fasta
color = blue
size = 9
zoom = chr_2:9000-99000,chr_7:400000-8000000,chr_3:85250-9500000
scale = True
seq_fontsize = 20
x_label_fontsize = 20

Resulting Image :

Without a zoom :

[canvas]
title = My Karyoplot
background_color = white
width = 30
height = 25
constrained_layout = True
title_fontsize = 30

[sequence]
reference = $HOME/user/chromosome.fasta
color = black
size = 9
limitesize = 50000
scale = False
seq_fontsize = 20
x_label_fontsize = 20

Resulting Image :

A karyoplot with a bed file feature

[canvas]
title =
background_color = white
width = 30
height = 25
constrained_layout = True
title_fontsize = 30


[sequence]
reference = $HOME/user/chromosome.fasta
color = black
size = 9
limitesize = 2000000
scale = True
seq_fontsize = 18
x_label_fontsize = 25

[track_gene]
color = red
title = gene feature
type = none
size = 3
thickness = 400
data = $HOME/user/chromosomes_genes.bed.gz
datatype= Bed
background_color = lightgrey

Resulting Image :

A karyoplot with a gc type feature

[canvas]
title = My karyoplot
background_color = white
width = 30
height = 25
constrained_layout = True
title_fontsize = 30

[sequence]
reference = $HOME/user/chromosome.fasta
color = black
size = 9
limitesize = 4000000
scale = True
seq_fontsize = 20
x_label_fontsize = 20

[track_gc]
color = green
title = gc feature
graph_type = GC
gc_window_length=1000
gc_window_overlap=0
thickness = 0.5
size = 8
background_color = white
scaley = True
y_label_fontsize = 15

Resulting Image :

A typical karyoplot

When combining both of these configuration file we get the following :

[canvas]
title = Final Karyoplot
background_color = white
width = 30
height = 25
constrained_layout = True
title_fontsize = 30

[sequence]
reference = $HOME/user/chromosome.fasta
color = black
size = 9
zoom = chr_1:10000-10000000,chr_7:400000-8000000,chr_3:85250-9500000
scale = True
seq_fontsize = 14
x_label_fontsize = 20

[track_gene]
color = red
title = gene feature
type = none
size = 3
thickness = 400
data = $HOME/user/chromosomes_genes.bed.gz
datatype= Bed
background_color = lightgrey

[track_gc]
color = green
title = gc feature
graph_type = GC
gc_window_length=1000
gc_window_overlap=0
thickness = 0.5
size = 8
background_color = beige
scaley = True
y_label_fontsize = 18

Resulting Image :

The feature tracks will appear in the order it shows up in the configuration file, in the previous example the “gene” track appears before the “gc” track.