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Merge pull request #2341 from merenlab/kegg-mapping-graphics
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Mapping multiple orthologs graphics types
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@semiller10
semiller10 authored Sep 13, 2024
2 parents 833fb13 + 87e0d8f commit 465a18d
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Showing 3 changed files with 405 additions and 263 deletions.
165 changes: 107 additions & 58 deletions anvio/keggmapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,12 +144,11 @@ def map_contigs_database_kos(
draws all available pathway maps in the KEGG data directory.
color_hexcode : str, '#2ca02c'
This is the color, by default green, for reactions containing contigs database
KOs. Alternatively to a color hex code, the string, 'original', can be provided to use
the original color scheme of the reference map. In global maps, KOs are represented in
reaction lines, and in overview maps, KOs are represented in reaction arrows. The
foreground color of the lines and arrows is set. In standard maps, KOs are represented
in boxes, the background color of which is set.
This is the color, by default green, for reactions containing contigs database KOs.
Alternatively to a color hex code, the string, 'original', can be provided to use the
original color scheme of the reference map. In global and overview maps, KOs are
represented in reaction lines. The foreground color of lines is set. In standard maps,
KOs are represented in boxes, the background color of which is set, or lines.
draw_maps_lacking_kos : bool, False
If False, by default, only draw maps containing any of the KOs in the contigs database.
Expand Down Expand Up @@ -217,10 +216,9 @@ def map_genomes_storage_genome_kos(
color_hexcode : str, '#2ca02c'
This is the color, by default green, for reactions containing KOs in the genome.
Alternatively to a color hex code, the string, 'original', can be provided to use the
original color scheme of the reference map. In global maps, KOs are represented in
reaction lines, and in overview maps, KOs are represented in reaction arrows. The
foreground color of the lines and arrows is set. In standard maps, KOs are represented
in boxes, the background color of which is set.
original color scheme of the reference map. In global and overview maps, KOs are
represented in reaction lines. The foreground color of lines is set. In standard maps,
KOs are represented in boxes, the background color of which is set, or lines.
draw_maps_lacking_kos : bool, False
If False, by default, only draw maps containing any of the KOs in the genome. If True,
Expand Down Expand Up @@ -283,8 +281,8 @@ def map_contigs_databases_kos(
genomes or metagenomes).
A reaction on a map can correspond to one or more KOs, and a KO can annotate one or more
sequences in a contigs database. In global and overview maps, reaction arrows are colored,
whereas in standard maps, boxes alongside arrows are colored.
sequences in a contigs database. In global and overview maps, reaction lines are colored.
In standard maps, reaction boxes or lines are colored.
Parameters
==========
Expand Down Expand Up @@ -746,8 +744,9 @@ def map_pan_database_kos(
"""
Draw pathway maps, highlighting consensus KOs from the pan database.
In global and overview maps, KOs are represented as reaction arrows, whereas in standard
maps, KOs are represented as boxes, the background color of which is changed.
A reaction on a map can correspond to one or more KOs, and a KO can annotate one or more
sequences in a contigs database. In global and overview maps, reaction lines are colored.
In standard maps, reaction boxes or lines are colored.
Parameters
==========
Expand Down Expand Up @@ -1328,10 +1327,10 @@ def _draw_map_kos_single_color(
Select KOs, any of which in the map are colored.
color_hexcode : str
This is the color, by default green, for reactions containing provided KOs. In global
maps, KOs are represented in reaction lines, and in overview maps, KOs are represented
in reaction arrows. The foreground color of the lines and arrows is set. In standard
maps, KOs are represented in boxes, the background color of which is set.
This is the color, by default green, for reactions containing provided KOs. A reaction
on a map can correspond to one or more KOs, and a KO can annotate one or more sequences
in a contigs database. In global and overview maps, reaction lines are colored. In
standard maps, reaction boxes or lines are colored.
output_dir : str
Path to an existing output directory in which map PDF files are drawn.
Expand All @@ -1353,27 +1352,38 @@ def _draw_map_kos_single_color(
return False

# Set the color of Graphics elements for reactions containing select KOs. For other Graphics
# elements, change the 'fgcolor' attribute to a nonsense value to ensure that the elements
# with the prioritized color can be distinguished from other elements. Also, in overview
# maps, widen lines from the base map default of 1.0.
# elements, change the 'fgcolor' attribute to a nonsense value of '0' to ensure that the
# elements with the prioritized color can be distinguished from other elements. Also, in
# overview and standard maps, widen lines from the base map default of 1.0.
all_entries = pathway.get_entries(entry_type='ortholog')
select_uuids = [entry.uuid for entry in select_entries]
color_priority: Dict[str, Dict[Tuple[str, str], float]] = {'ortholog': {}}

for entry in all_entries:
if entry.uuid in select_uuids:
for uuid in entry.children['graphics']:
graphics: kgml.Graphics = pathway.uuid_element_lookup[uuid]
if pathway.is_global_map:
assert graphics.type == 'line'
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
elif pathway.is_overview_map:
assert graphics.type == 'line'
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
graphics.width = 5.0
else:
graphics.fgcolor = '#000000'
graphics.bgcolor = color_hexcode
if graphics.type == 'rectangle':
graphics.fgcolor = '#000000'
graphics.bgcolor = color_hexcode
elif graphics.type == 'line':
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
graphics.width = 5.0
else:
raise AssertionError(
"Ortholog entries are assumed to have Graphics elements of type "
"'rectangle' or 'line', not the encountered type, "
f"'{graphics.type}'."
)
else:
for uuid in entry.children['graphics']:
graphics: kgml.Graphics = pathway.uuid_element_lookup[uuid]
Expand All @@ -1382,16 +1392,20 @@ def _draw_map_kos_single_color(
# Set the color priority so that the colored reactions are prioritized for display on top.
# Recolor "unprioritized" reactions to a background color. In global and overview maps,
# recolor circles to reflect the colors of prioritized reactions involving the compounds.
color_priority: Dict[str, Dict[str, Dict[Tuple[str, str], float]]] = {}
if pathway.is_global_map:
color_priority = {'ortholog': {(color_hexcode, '#FFFFFF'): 1.0}}
color_priority['ortholog'] = {'line': {(color_hexcode, '#FFFFFF'): 1.0}}
recolor_unprioritized_entries = 'g'
color_associated_compounds = 'high'
elif pathway.is_overview_map:
color_priority = {'ortholog': {(color_hexcode, '#FFFFFF'): 1.0}}
color_priority['ortholog'] = {'line': {(color_hexcode, '#FFFFFF'): 1.0}}
recolor_unprioritized_entries = 'w'
color_associated_compounds = 'high'
else:
color_priority = {'ortholog': {('#000000', color_hexcode): 1.0}}
color_priority['ortholog'] = {
'rectangle': {('#000000', color_hexcode): 1.0},
'line': {(color_hexcode, '#FFFFFF'): 1.0}
}
recolor_unprioritized_entries = 'w'
color_associated_compounds = None
pathway.set_color_priority(
Expand Down Expand Up @@ -1447,43 +1461,62 @@ def _draw_map_kos_original_color(
if not select_entries and not draw_map_lacking_kos:
return False

# Set "secondary" colors of Graphics elements for reactions containing select KOs: white
# background color of lines or black foreground text of boxes. For other Graphics elements,
# change the 'fgcolor' attribute to a nonsense value to ensure that the elements with
# prioritized colors can be distinguished from other elements. Also, in overview maps, widen
# lines from the base map default of 1.0.
# Set "secondary" colors of ortholog Graphics elements for reactions containing select KOs:
# white background color of lines or black foreground text of rectangles. For other Graphics
# elements, change the 'fgcolor' attribute to a nonsense value to ensure that the elements
# with prioritized colors can be distinguished from other elements. Also, in overview and
# standard maps, widen lines from the base map default of 1.0.
all_entries = pathway.get_entries(entry_type='ortholog')
select_uuids = [entry.uuid for entry in select_entries]
prioritized_colors: List[Tuple[str, str]] = []
prioritized_colors: Dict[str, List[Tuple[str, str]]] = {}
for entry in all_entries:
if entry.uuid in select_uuids:
for uuid in entry.children['graphics']:
graphics: kgml.Graphics = pathway.uuid_element_lookup[uuid]
if pathway.is_global_map:
assert graphics.type == 'line'
graphics.bgcolor = '#FFFFFF'
elif pathway.is_overview_map:
assert graphics.type == 'line'
graphics.bgcolor = '#FFFFFF'
graphics.width = 5.0
else:
graphics.fgcolor = '#000000'
prioritized_colors.append((graphics.fgcolor, graphics.bgcolor))
if graphics.type == 'rectangle':
graphics.fgcolor = '#000000'
elif graphics.type == 'line':
graphics.bgcolor = '#FFFFFF'
graphics.width = 5.0
else:
raise AssertionError(
"Ortholog entries are assumed to have Graphics elements of type "
"'rectangle' or 'line', not the encountered type, "
f"'{graphics.type}'."
)
try:
graphics_type_prioritized_colors = prioritized_colors[graphics.type]
except:
prioritized_colors[graphics.type] = graphics_type_prioritized_colors = []
graphics_type_prioritized_colors.append((graphics.fgcolor, graphics.bgcolor))
else:
for uuid in entry.children['graphics']:
graphics: kgml.Graphics = pathway.uuid_element_lookup[uuid]
graphics.fgcolor = '0'

# By default, global maps but not overview and standard maps have reactions with more than
# one color. Give higher priority to reaction entries that are encountered later (occur
# further down in the KGML file), and would thus be rendered above earlier reactions.
seen = set()
prioritized_colors = [
colors for colors in prioritized_colors if not (colors in seen or seen.add(colors))
]
priorities = np.linspace(0, 1, len(prioritized_colors) + 1)[1: ]
ortholog_color_priority = {
colors: priority for colors, priority in zip(prioritized_colors, priorities)
}
color_priority = {'ortholog': ortholog_color_priority}
# By default, global maps but not overview and standard maps display reaction graphics in
# more than one color. Give higher priority to reaction entries that are encountered later
# (occur further down in the KGML file), and would thus be rendered above earlier reactions.
color_priority: Dict[str, Dict[str, Dict[Tuple[str, str], float]]] = {'ortholog': {}}
for graphics_type, graphics_type_prioritized_colors in prioritized_colors.items():
seen = set()
unique_prioritized_colors = [
colors for colors in graphics_type_prioritized_colors
if not (colors in seen or seen.add(colors))
]
priorities = np.linspace(0, 1, len(unique_prioritized_colors) + 1)[1: ]
graphics_type_color_priority = {
colors: priority for colors, priority in zip(unique_prioritized_colors, priorities)
}
color_priority['ortholog'][graphics_type] = graphics_type_color_priority

# Recolor "unprioritized" reactions to a background color. In global and overview maps,
# recolor circles to reflect the colors of prioritized reactions involving the compounds.
Expand Down Expand Up @@ -1588,7 +1621,8 @@ def _draw_map_kos_membership(
if not entries and not draw_map_lacking_kos:
return False

# Change the colors of the KO graphics. A reaction Entry can represent multiple KOs.
# Change the colors of the KO graphics. A reaction Entry can represent multiple KOs. Also,
# in overview and standard maps, widen lines from the base map default of 1.0.
color_hexcodes = list(color_priority)
for entry in entries:
source_names = []
Expand All @@ -1609,43 +1643,58 @@ def _draw_map_kos_membership(
for uuid in entry.children['graphics']:
graphics: kgml.Graphics = pathway.uuid_element_lookup[uuid]
if pathway.is_global_map:
assert graphics.type == 'line'
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
elif pathway.is_overview_map:
assert graphics.type == 'line'
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
# Widen colored lines in overview maps. The width of lines in the base map is
# 1.0.
graphics.width = 5.0
else:
graphics.fgcolor = '#000000'
graphics.bgcolor = color_hexcode
if graphics.type == 'rectangle':
graphics.fgcolor = '#000000'
graphics.bgcolor = color_hexcode
elif graphics.type == 'line':
graphics.fgcolor = color_hexcode
graphics.bgcolor = '#FFFFFF'
graphics.width = 5.0
else:
raise AssertionError(
"Ortholog entries are assumed to have Graphics elements of type "
f"'rectangle' or 'line', not the encountered type, '{graphics.type}'."
)

# Set the color priorities of entries for proper overlaying in the image. Recolor
# "unprioritized" KO graphics to a background color. In global and overview maps, recolor
# circles to reflect the colors of prioritized lines and arrows.
ortholog_color_priority: Dict[Tuple[str, str], float] = {}
# circles to reflect the colors of prioritized reactions involving the compounds.
ortholog_color_priority: Dict[str, Dict[Tuple[str, str], float]] = {}
if pathway.is_global_map:
ortholog_color_priority['line'] = line_color_priority = {}
for color_hexcode, priority in color_priority.items():
ortholog_color_priority[(color_hexcode, '#FFFFFF')] = priority
line_color_priority[(color_hexcode, '#FFFFFF')] = priority
pathway.set_color_priority(
{'ortholog': ortholog_color_priority},
recolor_unprioritized_entries='g',
color_associated_compounds='high',
colormap=colormap
)
elif pathway.is_overview_map:
ortholog_color_priority['line'] = line_color_priority = {}
for color_hexcode, priority in color_priority.items():
ortholog_color_priority[(color_hexcode, '#FFFFFF')] = priority
line_color_priority[(color_hexcode, '#FFFFFF')] = priority
pathway.set_color_priority(
{'ortholog': ortholog_color_priority},
recolor_unprioritized_entries='w',
color_associated_compounds='high',
colormap=colormap
)
else:
ortholog_color_priority['rectangle'] = rectangle_color_priority = {}
ortholog_color_priority['line'] = line_color_priority = {}
for color_hexcode, priority in color_priority.items():
ortholog_color_priority[('#000000', color_hexcode)] = priority
rectangle_color_priority[('#000000', color_hexcode)] = priority
line_color_priority[(color_hexcode, '#FFFFFF')] = priority
pathway.set_color_priority(
{'ortholog': ortholog_color_priority},
recolor_unprioritized_entries='w'
Expand Down
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