def plot(self, placement, togjson, outdir, cfg):
"""
plot a plcement in the tree
show all pplacer placements and the LCA and HCA node
as well as the inferred lineage
"""
from ete3 import NodeStyle, TreeStyle
from ete3 import CircleFace, TextFace, RectFace
logging.debug("Plotting trees now")
# with no X display this needs to be set
os.environ["QT_QPA_PLATFORM"] = "offscreen"
info = self.loadInfo(togjson)
def defaultNodeStyle():
return NodeStyle()
nodeStyles = defaultdict(defaultNodeStyle)
no = 0
for LCAp, HPAp in zip(placement["LCA"], placement["HPA"]):
plotpath = os.path.join(outdir, f"tree_{no}.png")
# make shallow copy
t = self.t
LCA = LCAp["node"]
HPA = HPAp["node"]
# define basic tree style
ts = TreeStyle()
# hide leave names
ts.show_leaf_name = False
ts.root_opening_factor = 1
# circular tree
ts.mode = "c"
ts.rotation = 210
ts.arc_start = 0 # 0 degrees = 3 o'clock
ts.arc_span = 350
highlightsize = 80
nodesize = 10
# define styles for special nodes
# at the moment hard coded, but could be accesible for the user
# LCA style
LCAstyle = NodeStyle()
LCAstyle["fgcolor"] = "#33a02c"
LCAstyle["bgcolor"] = "#b2df8a"
LCAstyle["size"] = highlightsize
# HPA style
HPAstyle = NodeStyle()
HPAstyle["fgcolor"] = "#1f78b4"
HPAstyle["bgcolor"] = "#a6cee3"
HPAstyle["size"] = highlightsize
# default node
defaultStyle = NodeStyle()
defaultStyle["fgcolor"] = "gray"
defaultStyle["size"] = nodesize
# add legend
ts.legend_position = 1
ts.legend.add_face(CircleFace(40, LCAstyle["fgcolor"]), column=1)
ts.legend.add_face(TextFace(f"LCA", fsize=50), column=2)
ts.legend.add_face(CircleFace(40, HPAstyle["fgcolor"]), column=1)
ts.legend.add_face(TextFace(f"HPA", fsize=50), column=2)
i = 1
ts.legend.add_face(TextFace(f"p = {i}", fsize=50), column=1)
while i > 0:
temp_face = RectFace(60,
10,
fgcolor=p_to_color(i),
bgcolor=p_to_color(i))
temp_face.margin_top = -4
ts.legend.add_face(temp_face, column=1)
i -= 0.01
ts.legend.add_face(TextFace(f"p = {cfg['minPlacementLikelyhood']}",
fsize=50),
column=1)
# add highlights for each placed protein
for n in t.traverse():
if n.name.startswith("PTHR"):
# set color based on posterior prob:
x = (info[n.name]["post_prob"] -
cfg["minPlacementLikelyhood"]) / (
1 - cfg["minPlacementLikelyhood"])
# orange to purple gradient from 0 to 1 posterior propability
he = p_to_color(x)
nodeStyles[he]["bgcolor"] = he
# define back color of locations
n.set_style(nodeStyles[he])
elif n.name == LCA:
n.set_style(LCAstyle)
elif n.name == HPA:
n.set_style(HPAstyle)
else:
n.set_style(defaultStyle)
# plot to disk
_ = t.render(plotpath, w=320, units="mm", tree_style=ts)
no = no + 1
def nodeLayoutFunc(node):
taxid = int(node.name)
if taxid in taxidsToKeep:
taxGroupName = ncbiTaxa.get_taxid_translator(
[taxid]
)[taxid] # There has to be an easier way to look up names...
row = None
rangeRows = None
print(len(ranges))
if (len(ranges) == 1):
row = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'] == ranges[0])]
assert (len(row) == len(ranges))
elif len(ranges) > 1:
row = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'] == 0)]
assert (len(row) == 1)
rangeRows = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'].isin(set(ranges)))]
else:
assert (False)
overallPval = float(row['Pvalue'].values[0])
name = TextFace("%s" % taxGroupName,
fsize=baseFontSize * 2.5)
name.tight_text = True
name.margin_left = 20
name.margin_right = 0
name.margin_top = 40
name.margin_bottom = 12
faces.add_face_to_node(name, node, column=0)
#print(rangeRows)
# For each range to be included in this plot, add a bar
for rangeId in ranges:
#print("rangeId = %s" % (rangeId))
rowForThisRange = None
if len(ranges) == 1:
rowForThisRange = row
else:
rowForThisRange = rangeRows[rangeRows['Range'] ==
rangeId]
assert (len(rowForThisRange) == 1)
# Extract p-value and "effect-size" (signed R^2)
effectSize = float(
rowForThisRange['EffectSize'].values[0])
pval = float(rowForThisRange['Pvalue'].values[0])
# Set bar-graph color and significance markers
barColor = ""
significanceMarker = ""
if (pval < significanceLevel):
significanceMarker = " %s" % unichr(0x2731)
if effectSize < 0:
barColor = "#1133ff"
else:
barColor = "#ff3311"
else: # not significant
if effectSize < 0:
barColor = "#b0b0f0"
else:
barColor = "#ccb090"
# Add the minus sign if needed
signChar = ""
if effectSize < 0:
signChar = unichr(
0x2212
) # minus sign (more legible than a hypen...)
v = RectFace(width=abs(effectSize) * barScale,
height=baseFontSize * 3.5,
fgcolor=barColor,
bgcolor=barColor,
label={
"text":
"%s%.2g %s" %
(signChar, abs(effectSize),
significanceMarker),
"fontsize":
baseFontSize * 1.8,
"color":
"black"
})
#v.rotation = -90
v.margin_top = 1
v.margin_left = 30
v.margin_right = 8
v.margin_bottom = 12
faces.add_face_to_node(v, node, column=0)
details = TextFace(
"N=%d" % row['NumSpecies'], fsize=baseFontSize *
1.5) #, fsize=baseFontSize) #, fstyle="italic")
details.background.color = "#dfdfdf"
details.margin_left = 6
details.margin_right = 20
#details.margin_top=5
#details.margin_bottom=0
faces.add_face_to_node(details, node, column=1)
nstyle = NodeStyle()
nstyle["size"] = 0
node.set_style(nstyle)