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Added argument to include loose hits in the heatmap #337

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Added argument to include loose hits in the heatmap #337

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18 changes: 10 additions & 8 deletions app/Heatmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,11 @@ class Heatmap(object):
This is a program that genreates a heatmap of multiple RGI analyses.
"""

def __init__(self, input, classification, frequency, output, cluster, display, debug):
def __init__(self, input, classification, frequency, include_loose,output, cluster, display, debug):
self.input = input
self.classification = classification
self.frequency = frequency
self.include_loose = include_loose
self.output = output
self.cluster = cluster
self.display = display
Expand Down Expand Up @@ -332,7 +333,7 @@ def run(self):
hsp = max(value.keys(), key=(lambda key: value[key]['bit_score']))

# Flag to exclude loose hits
if value[hsp]["type_match"] != "Loose":
if value[hsp]["type_match"] != "Loose" or self.include_loose:
topmodel = value[hsp]["model_name"]
tophits[topmodel] = value[hsp]["type_match"]

Expand Down Expand Up @@ -409,7 +410,7 @@ def run(self):
genelist = sorted(genelist)

# Create a dictionary that will convert type of hit to num. value
conversion = {"Perfect": 2, "Strict": 1}
conversion = {"Perfect": 3, "Strict": 2, "Loose": 1}

# Apply conversion so hit criteria is number based
for sample in genes:
Expand All @@ -428,7 +429,7 @@ def run(self):

# Fixed colourmap values (purple, teal, yellow)
cmap_values = [0, 1, 2, 3]
custom_cmap = matplotlib.colors.ListedColormap(['#4c0057', '#00948f', '#feed00'])
custom_cmap = matplotlib.colors.ListedColormap(['#000000', '#4c0057', '#00948f', '#feed00'])
norm = matplotlib.colors.BoundaryNorm(cmap_values, custom_cmap.N)

# If the classification option chosen:
Expand Down Expand Up @@ -848,15 +849,16 @@ def run(self):
print('Output file %s: AMR genes are listed in alphabetical order '
'and samples have been clustered hierarchically (see SciPy documentation). '
'Yellow represents a perfect hit, teal represents a strict hit, purple '
'represents no hit.' %(file_name))
'represents a loose hit, black represents no hit.' %(file_name))
elif self.cluster == 'genes':
print('Output file %s: AMR genes have been clustered hierarchically. '
'Yellow represents a perfect hit, teal represents a strict hit, purple '
'represents no hit.' %(file_name))
'represents a loose hit, black represents no hit.' %(file_name))
elif self.cluster == 'both':
print('Output file %s: AMR genes and samples have been clustered hierarchically '
'(see SciPy documentation). Yellow represents a perfect hit, teal represents a strict hit, purple '
'represents no hit.' %(file_name))
'represents a loose hit, black represents no hit.' %(file_name))
else:
print('Output file %s: Yellow represents a perfect hit, '
'teal represents a strict hit, purple represents no hit.' %(file_name))
'teal represents a strict hit, purple represents a loose hit,'
' black represents no hit.' %(file_name))
4 changes: 3 additions & 1 deletion app/MainBase.py
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Expand Up @@ -388,6 +388,8 @@ def heatmap_args(self):
help="The option to organize resistance genes based on a category.")
parser.add_argument('-f', '--frequency', dest="frequency", action="store_true",
help="Represent samples based on resistance profile.")
parser.add_argument('-l', '--include_loose', dest="include_loose", action="store_true",
help="Include loose predictions.")
parser.add_argument('-o', '--output', dest="output", default="RGI_heatmap",
help="Name for the output EPS and PNG files.\nThe number of files run will automatically \nbe appended to the end of the file name.(default={})".format('RGI_heatmap'))
parser.add_argument('-clus', '--cluster', dest="cluster", choices=("samples", "genes", "both"),
Expand All @@ -400,7 +402,7 @@ def heatmap_args(self):
return parser

def heatmap_run(self, args):
obj = Heatmap(args.input, args.classification, args.frequency,
obj = Heatmap(args.input, args.classification, args.frequency, args.include_loose,
args.output, args.cluster, args.display, args.debug)
obj.run()

Expand Down