-
Notifications
You must be signed in to change notification settings - Fork 2
expression_viz mod
Interactive graphics in iPython
import query.egrin2_query as e2q
import pymongo
client = pymongo.MongoClient('baligadev')
db = client['mtu_db']
There are several dependencies that need to be satisfied, including:
-
pymongo
-
numpy
-
pandas
-
joblib
-
scipy
-
statsmodels
-
itertools
corem_genes = e2q.find_corem_info(db, x=["Rv0350","Rv0440"], x_type="corem_id", y_type="rows") print corem_genes #corem_genes.sort() #for i in corem_genes:
AttributeError Traceback (most recent call last)
in () ----> 1 corem_genes = e2q.find_corem_info(db, x=["Rv0350","Rv0440"], x_type="corem_id", y_type="rows") 2 print corem_genes 3 #corem_genes.sort() 4 #for i in corem_genes: 5 # print i + " is also called " + row2id( i, host="localhost", db="mtu_db", return_field = "name" )
/users/wwu/egrin2-tools/query/egrin2_query.pyc in find_corem_info(db, x, x_type, x_input_type, y_type, y_return_field, count, logic) 671 return None 672 else: --> 673 to_r = row2id_batch(db, query.rows[0], return_field=y_return_field, input_type="row_id") 674 675 elif y_type == "cols.col_id":
/usr/lib/python2.7/dist-packages/pandas/core/generic.pyc in getattr(self, name) 1813 return self[name] 1814 raise AttributeError("'%s' object has no attribute '%s'" % -> 1815 (type(self).name, name)) 1816 1817 def setattr(self, name, value):
AttributeError: 'DataFrame' object has no attribute 'rows'
corem_conditions = coremFinder(x = 1,x_type = "corem_id", y_type="conds",host="localhost",db="eco_db") corem_conditions.sort() for i in corem_conditions[0:5]: print i print "\nThere are %s other conditions in which these genes are co-regulated" % len(corem_conditions)
ATCC25404_wt_24hr_biofilm ATCC25404_wt_R1drd19_24hr_biofilm B178_mutant_Hsp60 B178_wt_Hsp60 BW25113_30C_biofilm
There are 418 other conditions in which these genes are co-regulated
gene_expression = expressionFinder(rows=corem_genes,cols=range(250),host="localhost",db="mtu_db")
line_plot = plotExpression( gene_expression, plot_type = "line", ipynb = True, sort = False ) py.iplot( line_plot )
line_plot = plotExpression( gene_expression, plot_type = "line", ipynb = True, sort = True )
py.iplot( line_plot )
heatmap = plotExpression( gene_expression, plot_type = "heatmap", ipynb = True )
py.iplot( heatmap )
boxplot = plotExpression( gene_expression, plot_type = "boxplot", ipynb = True )
py.iplot( boxplot )
boxplot = plotExpression( gene_expression.iloc[ :,range( 10 ) ], plot_type = "boxplot", ipynb = True )
py.iplot( boxplot )