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added option to keep sequence names in mini alignments
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@KatyBrown
KatyBrown committed Jul 18, 2024
1 parent 59d1ab5 commit 4a74f1c
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Showing 4 changed files with 56 additions and 37 deletions.
8 changes: 7 additions & 1 deletion CIAlign/argP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -549,7 +549,13 @@ def getParser():
is switched on) the rows will be labelled \
based on the input alignment, rather \
than renumbered. Default: %(default)s")

optional.add("--plot_keep_names", dest="plot_keep_names",
action="store_true",
help="If specified, rows in mini alignments will \
be named as in the original file, \
rather than numbered. Note that in many cases \
this is impractical in terms of making the image \
a reasonable height. Default: %(default)s")
optional.add("--plot_force_numbers", dest="plot_force_numbers",
action="store_true",
help="Force all rows to be numbered on the mini alignments \
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43 changes: 27 additions & 16 deletions CIAlign/miniAlignments.py
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Original file line number Diff line number Diff line change
Expand Up @@ -250,7 +250,8 @@ def drawMarkUpLegend(outfile, palette="CBS"):
def drawMiniAlignment(arr, nams, log, outfile, typ, plot_type='standard',
dpi=300, title=None, width=5, height=3, markup=False,
markupdict=None, ret=False, orig_nams=[],
keep_numbers=False, force_numbers=False, palette="CBS",
keep_numbers=False, keep_nams=False,
force_numbers=False, palette="CBS",
plot_identity_palette='bone',
plot_identity_gap_col='white',
plot_similarity_palette='bone',
Expand Down Expand Up @@ -310,6 +311,8 @@ def drawMiniAlignment(arr, nams, log, outfile, typ, plot_type='standard',
keep_numbers: bool
Number the sequences (rows) based on the original CIAlign input rather
than renumbering.
keep_names: bool
Show sequence names rather than numbers.
palette: str
Colour palette, CBS or Bright
plot_identity_palette: str
Expand Down Expand Up @@ -396,22 +399,30 @@ def drawMiniAlignment(arr, nams, log, outfile, typ, plot_type='standard',
f.suptitle(title, fontsize=fontsize*1.5, y=0.92)
for t in a.get_xticklabels():
t.set_fontsize(fontsize)
a.set_yticks(np.arange(ali_height-1, -1, -tickint))
x = 1
if tickint == 1:
if keep_numbers:
labs = []
for nam in orig_nams:
if nam in nams:
labs.append(x)
x += 1
a.set_yticklabels(labs,
fontsize=fontsize*0.75)
else:
a.set_yticklabels(np.arange(1, ali_height+1, tickint),
fontsize=fontsize*0.75)

if keep_nams:
a.set_yticks(np.arange(ali_height-1, -1, -1))
a.set_yticklabels(nams, fontsize=fontsize)
else:
a.set_yticklabels(np.arange(0, ali_height, tickint), fontsize=fontsize)
a.set_yticks(np.arange(ali_height-1, -1, -tickint))
x = 1
if tickint == 1:
if keep_numbers:
labs = []
for nam in orig_nams:
if nam in nams:
labs.append(x)
x += 1
a.set_yticklabels(labs,
fontsize=fontsize*0.75)
elif not keep_nams:
a.set_yticklabels(np.arange(1, ali_height+1, tickint),
fontsize=fontsize*0.75)

else:
if not keep_nams:
a.set_yticklabels(np.arange(0, ali_height, tickint),
fontsize=fontsize)

if markup:
a = drawMarkUp(a, markupdict, nams, ali_width, ali_height, palette)
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41 changes: 21 additions & 20 deletions CIAlign/runCIAlign.py
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Original file line number Diff line number Diff line change
Expand Up @@ -829,6 +829,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
Either 'aa' - amino acid - or 'nt' - nucleotide
'''
fn = args.plot_force_numbers
kn = args.plot_keep_numbers

# Mini alignment of CIAlign input
if args.plot_input or args.all_options or args.visualise:
log.info("Plotting mini alignment for input")
Expand All @@ -839,6 +841,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
outf, typ,
dpi=args.plot_dpi,
title=False,
keep_numbers=kn,
keep_nams=args.plot_keep_names,
width=args.plot_width,
height=args.plot_height,
force_numbers=fn,
Expand All @@ -850,26 +854,17 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
if not args.silent:
print("Plotting mini alignment for output")
outf = "%s_output.%s" % (args.outfile_stem, args.plot_format)
if not args.plot_keep_numbers:
miniAlignments.drawMiniAlignment(arr, nams, log,
outf, typ,
dpi=args.plot_dpi,
title=False,
width=args.plot_width,
height=args.plot_height,
force_numbers=fn,
palette=args.palette)
else:
miniAlignments.drawMiniAlignment(arr, nams, log,
outf, typ,
dpi=args.plot_dpi,
title=False,
width=args.plot_width,
height=args.plot_height,
orig_nams=orig_nams,
keep_numbers=True,
force_numbers=fn,
palette=args.palette)
miniAlignments.drawMiniAlignment(arr, nams, log,
outf, typ,
dpi=args.plot_dpi,
title=False,
keep_numbers=kn,
keep_nams=args.plot_keep_names,
width=args.plot_width,
height=args.plot_height,
force_numbers=fn,
palette=args.palette)

# Markup plot
# todo: what if only interpret functions are called?
if args.plot_markup or args.all_options or args.visualise:
Expand All @@ -881,6 +876,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
outf, typ,
dpi=args.plot_dpi,
title=False,
keep_numbers=kn,
keep_nams=args.plot_keep_names,
width=args.plot_width,
height=args.plot_height,
markup=True,
Expand All @@ -899,6 +896,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
plot_type='identity',
dpi=args.plot_dpi,
title=False,
keep_numbers=kn,
keep_nams=args.plot_keep_names,
width=args.plot_width,
height=args.plot_height,
force_numbers=fn,
Expand All @@ -918,6 +917,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
plot_type='similarity',
dpi=args.plot_dpi,
title=False,
keep_numbers=kn,
keep_nams=args.plot_keep_names,
width=args.plot_width,
height=args.plot_height,
force_numbers=fn,
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1 change: 1 addition & 0 deletions man/pages/usage.md
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Original file line number Diff line number Diff line change
Expand Up @@ -237,6 +237,7 @@ Output files:
| *`--plot_width`* | Mini alignment width in inches | 5 |
| *`--plot_height`* | Mini alignment height in inches | 3 |
| *`--plot_keep_numbers`* | Label rows in mini alignments based on input alignment, rather than renumbering | False |
| *`--plot_keep_names`* | Label rows in mini alignments with names from the original alignment, rather than numbers. This can be impractical for large alignments as the labels will overlap | False |
| *`--plot_force_numbers`* | Force all rows in mini alignments to be numbered rather than labelling e.g. every 10th row for larger plots Will cause labels to overlap in larger plots | False |
| *`--plot_sub_matrix_name`* | Substitution matrix to use for similarity plots | BLOSUM62 for amino acid, NUC.4.4 for nucleotide |
| *`--plot_identity_palette`* | Matplotlib palette name for identity mini alignments. | bone |
Expand Down

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