def singleTablePlot_mpl(parser, args):
''' kmerdict is a defaultdict(int)
It can take both empty and non-empty kmerdicts
returns update of the input kmerdict given the input string and k'''
kmerdict = kmercount_in_table(args.table1)
data = defaultdict(list)
numKmers = len(kmerdict)
for k in sorted(kmerdict.keys()):
data['kmers'].append(k)
data['counts'].append(kmerdict[k])
plt.bar(left=range(1,numKmers+1), height=data['counts'], width=1.0)
plt.show()
def singleTablePlot_mpl(parser, args):
''' kmerdict is a defaultdict(int)
It can take both empty and non-empty kmerdicts
returns update of the input kmerdict given the input string and k'''
kmerdict = kmercount_in_table(args.table1)
data = defaultdict(list)
numKmers = len(kmerdict)
for k in sorted(kmerdict.keys()):
data['kmers'].append(k)
data['counts'].append(kmerdict[k])
plt.bar(left=range(1, numKmers + 1), height=data['counts'], width=1.0)
plt.show()
def singleTablePlot_gg(parser, args):
''' kmerdict is a defaultdict(int)
It can take both empty and non-empty kmerdicts
returns update of the input kmerdict given the input string and k'''
r = robjects.r
r.library("ggplot2")
grdevices = importr('grDevices')
kmerdict = kmercount_in_table(args.table1)
data = defaultdict(list)
numKmers = len(kmerdict)
for k in sorted(kmerdict.keys()):
data['kmers'].append(k)
data['counts'].append(kmerdict[k])
df = robjects.DataFrame(data)
gp = ggplot2.ggplot(df)
## pp = gp + ggplot2.geom_bar(stat="identity")
pp = gp + ggplot2.aes_string(x=range(1,numKmers+1),y=data['counts']) \
+ ggplot2.geom_bar(stat="identity") \
+ ggplot2.scale_x_continuous(name="kmer", breaks=0.5+(range(1,numKmers+1)), labels=kmers)
pp.plot()
print('Type enter to exit.')
raw_input()
def singleTablePlot_gg(parser, args):
''' kmerdict is a defaultdict(int)
It can take both empty and non-empty kmerdicts
returns update of the input kmerdict given the input string and k'''
r = robjects.r
r.library("ggplot2")
grdevices = importr('grDevices')
kmerdict = kmercount_in_table(args.table1)
data = defaultdict(list)
numKmers = len(kmerdict)
for k in sorted(kmerdict.keys()):
data['kmers'].append(k)
data['counts'].append(kmerdict[k])
df = robjects.DataFrame(data)
gp = ggplot2.ggplot(df)
## pp = gp + ggplot2.geom_bar(stat="identity")
pp = gp + ggplot2.aes_string(x=range(1,numKmers+1),y=data['counts']) \
+ ggplot2.geom_bar(stat="identity") \
+ ggplot2.scale_x_continuous(name="kmer", breaks=0.5+(range(1,numKmers+1)), labels=kmers)
pp.plot()
print('Type enter to exit.')
raw_input()
def readInTwoKmerTables(parser, args):
kmerdict1 = kmercount_in_table(args.table1)
kmerdict2 = kmercount_in_table(args.table2)
## ensure equal kmer sets
kmerdict1, kmerdict2 = ensureEqualKmerSets(kmerdict1, kmerdict2)
return kmerdict1, kmerdict2
def readInTwoKmerTables(parser, args):
kmerdict1 = kmercount_in_table(args.table1)
kmerdict2 = kmercount_in_table(args.table2)
## ensure equal kmer sets
kmerdict1, kmerdict2 = ensureEqualKmerSets(kmerdict1, kmerdict2)
return kmerdict1, kmerdict2
