Comments (8)
This can be done by setting the record's feature_level_height
to 0, which can be done at record creation of afterwards. Here is a minimal example:
from dna_features_viewer import GraphicFeature, GraphicRecord
import numpy as np
record = GraphicRecord(sequence_length=1000, features=[
GraphicFeature(
start=50 * i + np.random.randint(-20, 20),
end=50 * i + np.random.randint(30, 70),
strand= [-1, 1][i % 2],
color=["limegreen", "yellow", "cyan"][i % 3],
)
for i in range(20)
])
record.feature_level_height = 0 # <=====
ax, _ = record.plot(figure_width=10);
from dnafeaturesviewer.
Hey,
I was having the same issue. In the end I used illustrator to align the arrows to the line. This kind of defeats the point.
I'm posting this to emphasize that there is more interest for this option.
Other than that I enjoy the library!
from dnafeaturesviewer.
@ghutinet @FruityPerdix there may be a trick to do that I am not 100% sure I understand what the expected result is, do you have a screenshot/schema?
from dnafeaturesviewer.
This is what would be ideal:
from dnafeaturesviewer.
Thanks, that works to align the arrows! However the annotation heights are not updated and stay at weird places:
from dnafeaturesviewer.
I'm curious to know if there was ever a fix for this issue. I had to mess around with the label font size and labels_spacing settings to find a combination of values that resulted in all labels being attached to lines.
from dnafeaturesviewer.
This problem is a bit complicated and may need refactoring, but redefining the below function before plotting at least connects the boxes until a proper solution is implemented:
def new_determine_annotation_height(levels):
return 1
record.determine_annotation_height = new_determine_annotation_height
from dnafeaturesviewer.
How about circular genomes?
from dnafeaturesviewer.
Related Issues (20)
- Cannot apply sequence translation on plot_on_multiple_lines or plot_on_multiple_pages HOT 2
- BiopythonTranslator: SeqFeatures with location_operator='join' get wrong position
- Labels overlap whan sharing axis HOT 2
- Feature request: x_lim best-fit HOT 6
- Enhanced Bokeh support for multiple plots HOT 2
- Linking exon annotations with intron lines, and other things. HOT 5
- Add an example which plots sequence features not starting from 0 HOT 5
- truncated scaffolds from gff files HOT 4
- figure is not coming
- type hints support HOT 1
- Error on BioPython v1.8.0 HOT 9
- type error for global variable related to BioPython update HOT 2
- sequences display from 1 not 0 ? HOT 1
- How to solve the memory problem of batch plotting? HOT 3
- Overlapping arrows in circular DNA HOT 1
- CircularGraphicRecord does not work. Unable to make circular graphs HOT 1
- UndefinedSequenceError with gff files and BioPython 1.81
- Oval or diamond/octagon in addition to arrows for displayed features? HOT 1
- 'Seq' object has no attribute 'defined' HOT 2
- feature location in a join, how to correnctly translate HOT 3
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