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adding no text option #39

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merged 4 commits into from
Apr 12, 2024
Merged

adding no text option #39

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f6f6142
adding no text option
aineniamh Apr 12, 2024
38f4eaf
remove st
aineniamh Apr 12, 2024
20006e1
add back in (not merging properly for some reason )
aineniamh Apr 12, 2024
4b7bb61
Merge branch 'master' into prior-to-reversion
aineniamh Apr 12, 2024
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2 changes: 2 additions & 0 deletions snipit/command.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ def main(sysargs = sys.argv[1:]):
f_group.add_argument("--high-to-low", action='store_false',
help="If sorted by mutation number is selected, show the sequences with the fewest SNPs closest to the reference. Default: False",
dest="high_to_low")
f_group.add_argument("--remove-site-text",action='store_true',help="Do not annotate text on the individual columns in the figure.",dest="remove_site_text")

s_group = parser.add_argument_group('SNP options')
s_group.add_argument("--show-indels",action='store_true',help="Include insertion and deletion mutations in snipit plot.",dest="show_indels")
Expand Down Expand Up @@ -120,6 +121,7 @@ def main(sysargs = sys.argv[1:]):
args.height,
args.size_option,
args.solid_background,
args.remove_site_text,
args.flip_vertical,
args.included_positions,
args.excluded_positions,
Expand Down
12 changes: 8 additions & 4 deletions snipit/scripts/snp_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,6 +358,8 @@ def make_graph(num_seqs,
height,
size_option,
solid_background,
ambig_mode,
remove_site_text,
flip_vertical=False,
included_positions=None,
excluded_positions=None,
Expand Down Expand Up @@ -552,7 +554,8 @@ def make_graph(num_seqs,

# write text adjacent to the SNPs shown with the numeric position
# the text alignment is toggled right/left (top/bottom considering 90-deg rotation) if the plot is flipped
ax.text(position, y_level+(0.55*y_inc), snp, size=9, ha="center", va="bottom" if not flip_vertical else "top", rotation=90)
if not remove_site_text:
ax.text(position, y_level+(0.55*y_inc), snp, size=9, ha="center", va="bottom" if not flip_vertical else "top", rotation=90)

# snp position labels
left_of_box = position-(0.4*spacing)
Expand All @@ -576,11 +579,12 @@ def make_graph(num_seqs,
ax.add_patch(rect)

# sequence variant text
ax.text(position, y_pos*y_inc, var, size=9, ha="center", va="center")
if not remove_site_text:
ax.text(position, y_pos*y_inc, var, size=9, ha="center", va="center")

# reference variant text

ax.text(position, y_inc * -0.2, ref, size=9, ha="center", va="center")
if not remove_site_text:
ax.text(position, y_inc * -0.2, ref, size=9, ha="center", va="center")

#polygon showing mapping from genome to spaced out snps
x = [snp-0.5,snp+0.5,right_of_box,left_of_box,snp-0.5]
Expand Down
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