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1 | # -*- coding: utf-8 -*- |
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1 | # -*- coding: utf-8 -*- | |
2 | """ |
|
2 | """ | |
3 | ====== |
|
3 | ====== | |
4 | Rmagic |
|
4 | Rmagic | |
5 | ====== |
|
5 | ====== | |
6 |
|
6 | |||
7 | Magic command interface for interactive work with R via rpy2 |
|
7 | Magic command interface for interactive work with R via rpy2 | |
8 |
|
8 | |||
9 | Usage |
|
9 | Usage | |
10 | ===== |
|
10 | ===== | |
11 |
|
11 | |||
12 | ``%R`` |
|
12 | ``%R`` | |
13 |
|
13 | |||
14 | {R_DOC} |
|
14 | {R_DOC} | |
15 |
|
15 | |||
16 | ``%Rpush`` |
|
16 | ``%Rpush`` | |
17 |
|
17 | |||
18 | {RPUSH_DOC} |
|
18 | {RPUSH_DOC} | |
19 |
|
19 | |||
20 | ``%Rpull`` |
|
20 | ``%Rpull`` | |
21 |
|
21 | |||
22 | {RPULL_DOC} |
|
22 | {RPULL_DOC} | |
23 |
|
23 | |||
24 | ``%Rget`` |
|
24 | ``%Rget`` | |
25 |
|
25 | |||
26 | {RGET_DOC} |
|
26 | {RGET_DOC} | |
27 |
|
27 | |||
28 | """ |
|
28 | """ | |
29 |
|
29 | |||
30 | #----------------------------------------------------------------------------- |
|
30 | #----------------------------------------------------------------------------- | |
31 | # Copyright (C) 2012 The IPython Development Team |
|
31 | # Copyright (C) 2012 The IPython Development Team | |
32 | # |
|
32 | # | |
33 | # Distributed under the terms of the BSD License. The full license is in |
|
33 | # Distributed under the terms of the BSD License. The full license is in | |
34 | # the file COPYING, distributed as part of this software. |
|
34 | # the file COPYING, distributed as part of this software. | |
35 | #----------------------------------------------------------------------------- |
|
35 | #----------------------------------------------------------------------------- | |
36 |
|
36 | |||
37 | import sys |
|
37 | import sys | |
38 | import tempfile |
|
38 | import tempfile | |
39 | from glob import glob |
|
39 | from glob import glob | |
40 | from shutil import rmtree |
|
40 | from shutil import rmtree | |
41 | from getopt import getopt |
|
41 | from getopt import getopt | |
42 |
|
42 | |||
43 | # numpy and rpy2 imports |
|
43 | # numpy and rpy2 imports | |
44 |
|
44 | |||
45 | import numpy as np |
|
45 | import numpy as np | |
46 |
|
46 | |||
47 | import rpy2.rinterface as ri |
|
47 | import rpy2.rinterface as ri | |
48 | import rpy2.robjects as ro |
|
48 | import rpy2.robjects as ro | |
49 | from rpy2.robjects.numpy2ri import numpy2ri |
|
49 | try: | |
50 | ro.conversion.py2ri = numpy2ri |
|
50 | from rpy2.robjects import pandas2ri | |
|
51 | pandas2ri.activate() | |||
|
52 | except ImportError: | |||
|
53 | pandas2ri = None | |||
|
54 | from rpy2.robjects import numpy2ri | |||
|
55 | numpy2ri.activate() | |||
51 |
|
56 | |||
52 | # IPython imports |
|
57 | # IPython imports | |
53 |
|
58 | |||
54 | from IPython.core.displaypub import publish_display_data |
|
59 | from IPython.core.displaypub import publish_display_data | |
55 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, |
|
60 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, | |
56 | line_cell_magic, needs_local_scope) |
|
61 | line_cell_magic, needs_local_scope) | |
57 | from IPython.testing.skipdoctest import skip_doctest |
|
62 | from IPython.testing.skipdoctest import skip_doctest | |
58 | from IPython.core.magic_arguments import ( |
|
63 | from IPython.core.magic_arguments import ( | |
59 | argument, magic_arguments, parse_argstring |
|
64 | argument, magic_arguments, parse_argstring | |
60 | ) |
|
65 | ) | |
|
66 | from IPython.external.simplegeneric import generic | |||
61 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 |
|
67 | from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3 | |
62 |
|
68 | |||
63 | class RInterpreterError(ri.RRuntimeError): |
|
69 | class RInterpreterError(ri.RRuntimeError): | |
64 | """An error when running R code in a %%R magic cell.""" |
|
70 | """An error when running R code in a %%R magic cell.""" | |
65 | def __init__(self, line, err, stdout): |
|
71 | def __init__(self, line, err, stdout): | |
66 | self.line = line |
|
72 | self.line = line | |
67 | self.err = err.rstrip() |
|
73 | self.err = err.rstrip() | |
68 | self.stdout = stdout.rstrip() |
|
74 | self.stdout = stdout.rstrip() | |
69 |
|
75 | |||
70 | def __unicode__(self): |
|
76 | def __unicode__(self): | |
71 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ |
|
77 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
72 | (self.line, self.err) |
|
78 | (self.line, self.err) | |
73 | if self.stdout and (self.stdout != self.err): |
|
79 | if self.stdout and (self.stdout != self.err): | |
74 | s += '\nR stdout:\n' + self.stdout |
|
80 | s += '\nR stdout:\n' + self.stdout | |
75 | return s |
|
81 | return s | |
76 |
|
82 | |||
77 | if PY3: |
|
83 | if PY3: | |
78 | __str__ = __unicode__ |
|
84 | __str__ = __unicode__ | |
79 | else: |
|
85 | else: | |
80 | def __str__(self): |
|
86 | def __str__(self): | |
81 | return unicode_to_str(unicode(self), 'utf-8') |
|
87 | return unicode_to_str(unicode(self), 'utf-8') | |
82 |
|
88 | |||
83 | def Rconverter(Robj, dataframe=False): |
|
89 | def Rconverter(Robj, dataframe=False): | |
84 | """ |
|
90 | """ | |
85 | Convert an object in R's namespace to one suitable |
|
91 | Convert an object in R's namespace to one suitable | |
86 | for ipython's namespace. |
|
92 | for ipython's namespace. | |
87 |
|
93 | |||
88 | For a data.frame, it tries to return a structured array. |
|
94 | For a data.frame, it tries to return a structured array. | |
89 | It first checks for colnames, then names. |
|
95 | It first checks for colnames, then names. | |
90 | If all are NULL, it returns np.asarray(Robj), else |
|
96 | If all are NULL, it returns np.asarray(Robj), else | |
91 | it tries to construct a recarray |
|
97 | it tries to construct a recarray | |
92 |
|
98 | |||
93 | Parameters |
|
99 | Parameters | |
94 | ---------- |
|
100 | ---------- | |
95 |
|
101 | |||
96 | Robj: an R object returned from rpy2 |
|
102 | Robj: an R object returned from rpy2 | |
97 | """ |
|
103 | """ | |
98 | is_data_frame = ro.r('is.data.frame') |
|
104 | is_data_frame = ro.r('is.data.frame') | |
99 | colnames = ro.r('colnames') |
|
105 | colnames = ro.r('colnames') | |
100 | rownames = ro.r('rownames') # with pandas, these could be used for the index |
|
106 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
101 | names = ro.r('names') |
|
107 | names = ro.r('names') | |
102 |
|
108 | |||
103 | if dataframe: |
|
109 | if dataframe: | |
104 | as_data_frame = ro.r('as.data.frame') |
|
110 | as_data_frame = ro.r('as.data.frame') | |
105 | cols = colnames(Robj) |
|
111 | cols = colnames(Robj) | |
106 | _names = names(Robj) |
|
112 | _names = names(Robj) | |
107 | if cols != ri.NULL: |
|
113 | if cols != ri.NULL: | |
108 | Robj = as_data_frame(Robj) |
|
114 | Robj = as_data_frame(Robj) | |
109 | names = tuple(np.array(cols)) |
|
115 | names = tuple(np.array(cols)) | |
110 | elif _names != ri.NULL: |
|
116 | elif _names != ri.NULL: | |
111 | names = tuple(np.array(_names)) |
|
117 | names = tuple(np.array(_names)) | |
112 | else: # failed to find names |
|
118 | else: # failed to find names | |
113 | return np.asarray(Robj) |
|
119 | return np.asarray(Robj) | |
114 | Robj = np.rec.fromarrays(Robj, names = names) |
|
120 | Robj = np.rec.fromarrays(Robj, names = names) | |
115 | return np.asarray(Robj) |
|
121 | return np.asarray(Robj) | |
116 |
|
122 | |||
|
123 | @generic | |||
117 | def pyconverter(pyobj): |
|
124 | def pyconverter(pyobj): | |
118 |
"""Convert Python objects to R objects. |
|
125 | """Convert Python objects to R objects. Add types using the decorator: | |
119 | if 'pandas' in sys.modules: |
|
|||
120 | # We only do this if pandas is already loaded |
|
|||
121 | from pandas import DataFrame |
|
|||
122 | if isinstance(pyobj, DataFrame): |
|
|||
123 | from pandas.rpy.common import convert_to_r_dataframe |
|
|||
124 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) |
|
|||
125 |
|
|
126 | ||
|
127 | @pyconverter.when_type | |||
|
128 | """ | |||
|
129 | return pyobj | |||
|
130 | ||||
|
131 | # The default conversion for lists seems to make them a nested list. That has | |||
|
132 | # some advantages, but is rarely convenient, so for interactive use, we convert | |||
|
133 | # lists to a numpy array, which becomes an R vector. | |||
|
134 | @pyconverter.when_type(list) | |||
|
135 | def pyconverter_list(pyobj): | |||
126 | return np.asarray(pyobj) |
|
136 | return np.asarray(pyobj) | |
127 |
|
137 | |||
|
138 | if pandas2ri is None: | |||
|
139 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' | |||
|
140 | # conversion function. | |||
|
141 | try: | |||
|
142 | from pandas import DataFrame | |||
|
143 | from pandas.rpy.common import convert_to_r_dataframe | |||
|
144 | @pyconverter.when_type(DataFrame) | |||
|
145 | def pyconverter_dataframe(pyobj): | |||
|
146 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) | |||
|
147 | except ImportError: | |||
|
148 | pass | |||
|
149 | ||||
128 | @magics_class |
|
150 | @magics_class | |
129 | class RMagics(Magics): |
|
151 | class RMagics(Magics): | |
130 | """A set of magics useful for interactive work with R via rpy2. |
|
152 | """A set of magics useful for interactive work with R via rpy2. | |
131 | """ |
|
153 | """ | |
132 |
|
154 | |||
133 | def __init__(self, shell, Rconverter=Rconverter, |
|
155 | def __init__(self, shell, Rconverter=Rconverter, | |
134 | pyconverter=pyconverter, |
|
156 | pyconverter=pyconverter, | |
135 | cache_display_data=False): |
|
157 | cache_display_data=False): | |
136 | """ |
|
158 | """ | |
137 | Parameters |
|
159 | Parameters | |
138 | ---------- |
|
160 | ---------- | |
139 |
|
161 | |||
140 | shell : IPython shell |
|
162 | shell : IPython shell | |
141 |
|
163 | |||
142 | Rconverter : callable |
|
164 | Rconverter : callable | |
143 | To be called on values taken from R before putting them in the |
|
165 | To be called on values taken from R before putting them in the | |
144 | IPython namespace. |
|
166 | IPython namespace. | |
145 |
|
167 | |||
146 | pyconverter : callable |
|
168 | pyconverter : callable | |
147 | To be called on values in ipython namespace before |
|
169 | To be called on values in ipython namespace before | |
148 | assigning to variables in rpy2. |
|
170 | assigning to variables in rpy2. | |
149 |
|
171 | |||
150 | cache_display_data : bool |
|
172 | cache_display_data : bool | |
151 | If True, the published results of the final call to R are |
|
173 | If True, the published results of the final call to R are | |
152 | cached in the variable 'display_cache'. |
|
174 | cached in the variable 'display_cache'. | |
153 |
|
175 | |||
154 | """ |
|
176 | """ | |
155 | super(RMagics, self).__init__(shell) |
|
177 | super(RMagics, self).__init__(shell) | |
156 | self.cache_display_data = cache_display_data |
|
178 | self.cache_display_data = cache_display_data | |
157 |
|
179 | |||
158 | self.r = ro.R() |
|
180 | self.r = ro.R() | |
159 |
|
181 | |||
160 | self.Rstdout_cache = [] |
|
182 | self.Rstdout_cache = [] | |
161 | self.pyconverter = pyconverter |
|
183 | self.pyconverter = pyconverter | |
162 | self.Rconverter = Rconverter |
|
184 | self.Rconverter = Rconverter | |
163 |
|
185 | |||
164 | def eval(self, line): |
|
186 | def eval(self, line): | |
165 | ''' |
|
187 | ''' | |
166 | Parse and evaluate a line with rpy2. |
|
188 | Parse and evaluate a line with rpy2. | |
167 | Returns the output to R's stdout() connection |
|
189 | Returns the output to R's stdout() connection | |
168 | and the value of eval(parse(line)). |
|
190 | and the value of eval(parse(line)). | |
169 | ''' |
|
191 | ''' | |
170 | old_writeconsole = ri.get_writeconsole() |
|
192 | old_writeconsole = ri.get_writeconsole() | |
171 | ri.set_writeconsole(self.write_console) |
|
193 | ri.set_writeconsole(self.write_console) | |
172 | try: |
|
194 | try: | |
173 | value = ri.baseenv['eval'](ri.parse(line)) |
|
195 | value = ri.baseenv['eval'](ri.parse(line)) | |
174 | except (ri.RRuntimeError, ValueError) as exception: |
|
196 | except (ri.RRuntimeError, ValueError) as exception: | |
175 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error |
|
197 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
176 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) |
|
198 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
177 | text_output = self.flush() |
|
199 | text_output = self.flush() | |
178 | ri.set_writeconsole(old_writeconsole) |
|
200 | ri.set_writeconsole(old_writeconsole) | |
179 | return text_output, value |
|
201 | return text_output, value | |
180 |
|
202 | |||
181 | def write_console(self, output): |
|
203 | def write_console(self, output): | |
182 | ''' |
|
204 | ''' | |
183 | A hook to capture R's stdout in a cache. |
|
205 | A hook to capture R's stdout in a cache. | |
184 | ''' |
|
206 | ''' | |
185 | self.Rstdout_cache.append(output) |
|
207 | self.Rstdout_cache.append(output) | |
186 |
|
208 | |||
187 | def flush(self): |
|
209 | def flush(self): | |
188 | ''' |
|
210 | ''' | |
189 | Flush R's stdout cache to a string, returning the string. |
|
211 | Flush R's stdout cache to a string, returning the string. | |
190 | ''' |
|
212 | ''' | |
191 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
213 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
192 | self.Rstdout_cache = [] |
|
214 | self.Rstdout_cache = [] | |
193 | return value |
|
215 | return value | |
194 |
|
216 | |||
195 | @skip_doctest |
|
217 | @skip_doctest | |
196 | @needs_local_scope |
|
218 | @needs_local_scope | |
197 | @line_magic |
|
219 | @line_magic | |
198 | def Rpush(self, line, local_ns=None): |
|
220 | def Rpush(self, line, local_ns=None): | |
199 | ''' |
|
221 | ''' | |
200 | A line-level magic for R that pushes |
|
222 | A line-level magic for R that pushes | |
201 | variables from python to rpy2. The line should be made up |
|
223 | variables from python to rpy2. The line should be made up | |
202 | of whitespace separated variable names in the IPython |
|
224 | of whitespace separated variable names in the IPython | |
203 | namespace:: |
|
225 | namespace:: | |
204 |
|
226 | |||
205 | In [7]: import numpy as np |
|
227 | In [7]: import numpy as np | |
206 |
|
228 | |||
207 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
229 | In [8]: X = np.array([4.5,6.3,7.9]) | |
208 |
|
230 | |||
209 | In [9]: X.mean() |
|
231 | In [9]: X.mean() | |
210 | Out[9]: 6.2333333333333343 |
|
232 | Out[9]: 6.2333333333333343 | |
211 |
|
233 | |||
212 | In [10]: %Rpush X |
|
234 | In [10]: %Rpush X | |
213 |
|
235 | |||
214 | In [11]: %R mean(X) |
|
236 | In [11]: %R mean(X) | |
215 | Out[11]: array([ 6.23333333]) |
|
237 | Out[11]: array([ 6.23333333]) | |
216 |
|
238 | |||
217 | ''' |
|
239 | ''' | |
218 | if local_ns is None: |
|
240 | if local_ns is None: | |
219 | local_ns = {} |
|
241 | local_ns = {} | |
220 |
|
242 | |||
221 | inputs = line.split(' ') |
|
243 | inputs = line.split(' ') | |
222 | for input in inputs: |
|
244 | for input in inputs: | |
223 | try: |
|
245 | try: | |
224 | val = local_ns[input] |
|
246 | val = local_ns[input] | |
225 | except KeyError: |
|
247 | except KeyError: | |
226 | try: |
|
248 | try: | |
227 | val = self.shell.user_ns[input] |
|
249 | val = self.shell.user_ns[input] | |
228 | except KeyError: |
|
250 | except KeyError: | |
229 | # reraise the KeyError as a NameError so that it looks like |
|
251 | # reraise the KeyError as a NameError so that it looks like | |
230 | # the standard python behavior when you use an unnamed |
|
252 | # the standard python behavior when you use an unnamed | |
231 | # variable |
|
253 | # variable | |
232 | raise NameError("name '%s' is not defined" % input) |
|
254 | raise NameError("name '%s' is not defined" % input) | |
233 |
|
255 | |||
234 | self.r.assign(input, self.pyconverter(val)) |
|
256 | self.r.assign(input, self.pyconverter(val)) | |
235 |
|
257 | |||
236 | @skip_doctest |
|
258 | @skip_doctest | |
237 | @magic_arguments() |
|
259 | @magic_arguments() | |
238 | @argument( |
|
260 | @argument( | |
239 | '-d', '--as_dataframe', action='store_true', |
|
261 | '-d', '--as_dataframe', action='store_true', | |
240 | default=False, |
|
262 | default=False, | |
241 | help='Convert objects to data.frames before returning to ipython.' |
|
263 | help='Convert objects to data.frames before returning to ipython.' | |
242 | ) |
|
264 | ) | |
243 | @argument( |
|
265 | @argument( | |
244 | 'outputs', |
|
266 | 'outputs', | |
245 | nargs='*', |
|
267 | nargs='*', | |
246 | ) |
|
268 | ) | |
247 | @line_magic |
|
269 | @line_magic | |
248 | def Rpull(self, line): |
|
270 | def Rpull(self, line): | |
249 | ''' |
|
271 | ''' | |
250 | A line-level magic for R that pulls |
|
272 | A line-level magic for R that pulls | |
251 | variables from python to rpy2:: |
|
273 | variables from python to rpy2:: | |
252 |
|
274 | |||
253 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
275 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
254 |
|
276 | |||
255 | In [19]: %Rpull x y z |
|
277 | In [19]: %Rpull x y z | |
256 |
|
278 | |||
257 | In [20]: x |
|
279 | In [20]: x | |
258 | Out[20]: array([ 3. , 4. , 6.7]) |
|
280 | Out[20]: array([ 3. , 4. , 6.7]) | |
259 |
|
281 | |||
260 | In [21]: y |
|
282 | In [21]: y | |
261 | Out[21]: array([ 4., 6., 7.]) |
|
283 | Out[21]: array([ 4., 6., 7.]) | |
262 |
|
284 | |||
263 | In [22]: z |
|
285 | In [22]: z | |
264 | Out[22]: |
|
286 | Out[22]: | |
265 | array(['a', '3', '4'], |
|
287 | array(['a', '3', '4'], | |
266 | dtype='|S1') |
|
288 | dtype='|S1') | |
267 |
|
289 | |||
268 |
|
290 | |||
269 | If --as_dataframe, then each object is returned as a structured array |
|
291 | If --as_dataframe, then each object is returned as a structured array | |
270 | after first passed through "as.data.frame" in R before |
|
292 | after first passed through "as.data.frame" in R before | |
271 | being calling self.Rconverter. |
|
293 | being calling self.Rconverter. | |
272 | This is useful when a structured array is desired as output, or |
|
294 | This is useful when a structured array is desired as output, or | |
273 | when the object in R has mixed data types. |
|
295 | when the object in R has mixed data types. | |
274 | See the %%R docstring for more examples. |
|
296 | See the %%R docstring for more examples. | |
275 |
|
297 | |||
276 | Notes |
|
298 | Notes | |
277 | ----- |
|
299 | ----- | |
278 |
|
300 | |||
279 | Beware that R names can have '.' so this is not fool proof. |
|
301 | Beware that R names can have '.' so this is not fool proof. | |
280 | To avoid this, don't name your R objects with '.'s... |
|
302 | To avoid this, don't name your R objects with '.'s... | |
281 |
|
303 | |||
282 | ''' |
|
304 | ''' | |
283 | args = parse_argstring(self.Rpull, line) |
|
305 | args = parse_argstring(self.Rpull, line) | |
284 | outputs = args.outputs |
|
306 | outputs = args.outputs | |
285 | for output in outputs: |
|
307 | for output in outputs: | |
286 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) |
|
308 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
287 |
|
309 | |||
288 | @skip_doctest |
|
310 | @skip_doctest | |
289 | @magic_arguments() |
|
311 | @magic_arguments() | |
290 | @argument( |
|
312 | @argument( | |
291 | '-d', '--as_dataframe', action='store_true', |
|
313 | '-d', '--as_dataframe', action='store_true', | |
292 | default=False, |
|
314 | default=False, | |
293 | help='Convert objects to data.frames before returning to ipython.' |
|
315 | help='Convert objects to data.frames before returning to ipython.' | |
294 | ) |
|
316 | ) | |
295 | @argument( |
|
317 | @argument( | |
296 | 'output', |
|
318 | 'output', | |
297 | nargs=1, |
|
319 | nargs=1, | |
298 | type=str, |
|
320 | type=str, | |
299 | ) |
|
321 | ) | |
300 | @line_magic |
|
322 | @line_magic | |
301 | def Rget(self, line): |
|
323 | def Rget(self, line): | |
302 | ''' |
|
324 | ''' | |
303 | Return an object from rpy2, possibly as a structured array (if possible). |
|
325 | Return an object from rpy2, possibly as a structured array (if possible). | |
304 | Similar to Rpull except only one argument is accepted and the value is |
|
326 | Similar to Rpull except only one argument is accepted and the value is | |
305 | returned rather than pushed to self.shell.user_ns:: |
|
327 | returned rather than pushed to self.shell.user_ns:: | |
306 |
|
328 | |||
307 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
329 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
308 |
|
330 | |||
309 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
331 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
310 |
|
332 | |||
311 | In [5]: %R -i datapy |
|
333 | In [5]: %R -i datapy | |
312 |
|
334 | |||
313 | In [6]: %Rget datapy |
|
335 | In [6]: %Rget datapy | |
314 | Out[6]: |
|
336 | Out[6]: | |
315 | array([['1', '2', '3', '4'], |
|
337 | array([['1', '2', '3', '4'], | |
316 | ['2', '3', '2', '5'], |
|
338 | ['2', '3', '2', '5'], | |
317 | ['a', 'b', 'c', 'e']], |
|
339 | ['a', 'b', 'c', 'e']], | |
318 | dtype='|S1') |
|
340 | dtype='|S1') | |
319 |
|
341 | |||
320 | In [7]: %Rget -d datapy |
|
342 | In [7]: %Rget -d datapy | |
321 | Out[7]: |
|
343 | Out[7]: | |
322 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
344 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
323 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
345 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
324 |
|
346 | |||
325 | ''' |
|
347 | ''' | |
326 | args = parse_argstring(self.Rget, line) |
|
348 | args = parse_argstring(self.Rget, line) | |
327 | output = args.output |
|
349 | output = args.output | |
328 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) |
|
350 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
329 |
|
351 | |||
330 |
|
352 | |||
331 | @skip_doctest |
|
353 | @skip_doctest | |
332 | @magic_arguments() |
|
354 | @magic_arguments() | |
333 | @argument( |
|
355 | @argument( | |
334 | '-i', '--input', action='append', |
|
356 | '-i', '--input', action='append', | |
335 | help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.' |
|
357 | help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.' | |
336 | ) |
|
358 | ) | |
337 | @argument( |
|
359 | @argument( | |
338 | '-o', '--output', action='append', |
|
360 | '-o', '--output', action='append', | |
339 | help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.' |
|
361 | help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.' | |
340 | ) |
|
362 | ) | |
341 | @argument( |
|
363 | @argument( | |
342 | '-w', '--width', type=int, |
|
364 | '-w', '--width', type=int, | |
343 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
365 | help='Width of png plotting device sent as an argument to *png* in R.' | |
344 | ) |
|
366 | ) | |
345 | @argument( |
|
367 | @argument( | |
346 | '-h', '--height', type=int, |
|
368 | '-h', '--height', type=int, | |
347 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
369 | help='Height of png plotting device sent as an argument to *png* in R.' | |
348 | ) |
|
370 | ) | |
349 |
|
371 | |||
350 | @argument( |
|
372 | @argument( | |
351 | '-d', '--dataframe', action='append', |
|
373 | '-d', '--dataframe', action='append', | |
352 | help='Convert these objects to data.frames and return as structured arrays.' |
|
374 | help='Convert these objects to data.frames and return as structured arrays.' | |
353 | ) |
|
375 | ) | |
354 | @argument( |
|
376 | @argument( | |
355 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], |
|
377 | '-u', '--units', type=unicode, choices=["px", "in", "cm", "mm"], | |
356 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
378 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
357 | ) |
|
379 | ) | |
358 | @argument( |
|
380 | @argument( | |
359 | '-r', '--res', type=int, |
|
381 | '-r', '--res', type=int, | |
360 | help='Resolution of png plotting device sent as an argument to *png* in R. Defaults to 72 if *units* is one of ["in", "cm", "mm"].' |
|
382 | help='Resolution of png plotting device sent as an argument to *png* in R. Defaults to 72 if *units* is one of ["in", "cm", "mm"].' | |
361 | ) |
|
383 | ) | |
362 | @argument( |
|
384 | @argument( | |
363 | '-p', '--pointsize', type=int, |
|
385 | '-p', '--pointsize', type=int, | |
364 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
386 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
365 | ) |
|
387 | ) | |
366 | @argument( |
|
388 | @argument( | |
367 | '-b', '--bg', |
|
389 | '-b', '--bg', | |
368 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
390 | help='Background of png plotting device sent as an argument to *png* in R.' | |
369 | ) |
|
391 | ) | |
370 | @argument( |
|
392 | @argument( | |
371 | '-n', '--noreturn', |
|
393 | '-n', '--noreturn', | |
372 | help='Force the magic to not return anything.', |
|
394 | help='Force the magic to not return anything.', | |
373 | action='store_true', |
|
395 | action='store_true', | |
374 | default=False |
|
396 | default=False | |
375 | ) |
|
397 | ) | |
376 | @argument( |
|
398 | @argument( | |
377 | 'code', |
|
399 | 'code', | |
378 | nargs='*', |
|
400 | nargs='*', | |
379 | ) |
|
401 | ) | |
380 | @needs_local_scope |
|
402 | @needs_local_scope | |
381 | @line_cell_magic |
|
403 | @line_cell_magic | |
382 | def R(self, line, cell=None, local_ns=None): |
|
404 | def R(self, line, cell=None, local_ns=None): | |
383 | ''' |
|
405 | ''' | |
384 | Execute code in R, and pull some of the results back into the Python namespace. |
|
406 | Execute code in R, and pull some of the results back into the Python namespace. | |
385 |
|
407 | |||
386 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
408 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
387 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
409 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
388 | final line. |
|
410 | final line. | |
389 |
|
411 | |||
390 | Multiple R lines can be executed by joining them with semicolons:: |
|
412 | Multiple R lines can be executed by joining them with semicolons:: | |
391 |
|
413 | |||
392 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
414 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
393 | Out[9]: array([ 4.25]) |
|
415 | Out[9]: array([ 4.25]) | |
394 |
|
416 | |||
395 | As a cell, this will run a block of R code, without bringing anything back by default:: |
|
417 | As a cell, this will run a block of R code, without bringing anything back by default:: | |
396 |
|
418 | |||
397 | In [10]: %%R |
|
419 | In [10]: %%R | |
398 | ....: Y = c(2,4,3,9) |
|
420 | ....: Y = c(2,4,3,9) | |
399 | ....: print(summary(lm(Y~X))) |
|
421 | ....: print(summary(lm(Y~X))) | |
400 | ....: |
|
422 | ....: | |
401 |
|
423 | |||
402 | Call: |
|
424 | Call: | |
403 | lm(formula = Y ~ X) |
|
425 | lm(formula = Y ~ X) | |
404 |
|
426 | |||
405 | Residuals: |
|
427 | Residuals: | |
406 | 1 2 3 4 |
|
428 | 1 2 3 4 | |
407 | 0.88 -0.24 -2.28 1.64 |
|
429 | 0.88 -0.24 -2.28 1.64 | |
408 |
|
430 | |||
409 | Coefficients: |
|
431 | Coefficients: | |
410 | Estimate Std. Error t value Pr(>|t|) |
|
432 | Estimate Std. Error t value Pr(>|t|) | |
411 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
433 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
412 | X 1.0400 0.4822 2.157 0.164 |
|
434 | X 1.0400 0.4822 2.157 0.164 | |
413 |
|
435 | |||
414 | Residual standard error: 2.088 on 2 degrees of freedom |
|
436 | Residual standard error: 2.088 on 2 degrees of freedom | |
415 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
437 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
416 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
438 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
417 |
|
439 | |||
418 | In the notebook, plots are published as the output of the cell. |
|
440 | In the notebook, plots are published as the output of the cell. | |
419 |
|
441 | |||
420 | %R plot(X, Y) |
|
442 | %R plot(X, Y) | |
421 |
|
443 | |||
422 | will create a scatter plot of X bs Y. |
|
444 | will create a scatter plot of X bs Y. | |
423 |
|
445 | |||
424 | If cell is not None and line has some R code, it is prepended to |
|
446 | If cell is not None and line has some R code, it is prepended to | |
425 | the R code in cell. |
|
447 | the R code in cell. | |
426 |
|
448 | |||
427 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
449 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
428 |
|
450 | |||
429 | In [14]: Z = np.array([1,4,5,10]) |
|
451 | In [14]: Z = np.array([1,4,5,10]) | |
430 |
|
452 | |||
431 | In [15]: %R -i Z mean(Z) |
|
453 | In [15]: %R -i Z mean(Z) | |
432 | Out[15]: array([ 5.]) |
|
454 | Out[15]: array([ 5.]) | |
433 |
|
455 | |||
434 |
|
456 | |||
435 | In [16]: %R -o W W=Z*mean(Z) |
|
457 | In [16]: %R -o W W=Z*mean(Z) | |
436 | Out[16]: array([ 5., 20., 25., 50.]) |
|
458 | Out[16]: array([ 5., 20., 25., 50.]) | |
437 |
|
459 | |||
438 | In [17]: W |
|
460 | In [17]: W | |
439 | Out[17]: array([ 5., 20., 25., 50.]) |
|
461 | Out[17]: array([ 5., 20., 25., 50.]) | |
440 |
|
462 | |||
441 | The return value is determined by these rules: |
|
463 | The return value is determined by these rules: | |
442 |
|
464 | |||
443 | * If the cell is not None, the magic returns None. |
|
465 | * If the cell is not None, the magic returns None. | |
444 |
|
466 | |||
445 | * If the cell evaluates as False, the resulting value is returned |
|
467 | * If the cell evaluates as False, the resulting value is returned | |
446 | unless the final line prints something to the console, in |
|
468 | unless the final line prints something to the console, in | |
447 | which case None is returned. |
|
469 | which case None is returned. | |
448 |
|
470 | |||
449 | * If the final line results in a NULL value when evaluated |
|
471 | * If the final line results in a NULL value when evaluated | |
450 | by rpy2, then None is returned. |
|
472 | by rpy2, then None is returned. | |
451 |
|
473 | |||
452 | * No attempt is made to convert the final value to a structured array. |
|
474 | * No attempt is made to convert the final value to a structured array. | |
453 | Use the --dataframe flag or %Rget to push / return a structured array. |
|
475 | Use the --dataframe flag or %Rget to push / return a structured array. | |
454 |
|
476 | |||
455 | * If the -n flag is present, there is no return value. |
|
477 | * If the -n flag is present, there is no return value. | |
456 |
|
478 | |||
457 | * A trailing ';' will also result in no return value as the last |
|
479 | * A trailing ';' will also result in no return value as the last | |
458 | value in the line is an empty string. |
|
480 | value in the line is an empty string. | |
459 |
|
481 | |||
460 | The --dataframe argument will attempt to return structured arrays. |
|
482 | The --dataframe argument will attempt to return structured arrays. | |
461 | This is useful for dataframes with |
|
483 | This is useful for dataframes with | |
462 | mixed data types. Note also that for a data.frame, |
|
484 | mixed data types. Note also that for a data.frame, | |
463 | if it is returned as an ndarray, it is transposed:: |
|
485 | if it is returned as an ndarray, it is transposed:: | |
464 |
|
486 | |||
465 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
487 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
466 |
|
488 | |||
467 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
489 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
468 |
|
490 | |||
469 | In [20]: %%R -o datar |
|
491 | In [20]: %%R -o datar | |
470 | datar = datapy |
|
492 | datar = datapy | |
471 | ....: |
|
493 | ....: | |
472 |
|
494 | |||
473 | In [21]: datar |
|
495 | In [21]: datar | |
474 | Out[21]: |
|
496 | Out[21]: | |
475 | array([['1', '2', '3', '4'], |
|
497 | array([['1', '2', '3', '4'], | |
476 | ['2', '3', '2', '5'], |
|
498 | ['2', '3', '2', '5'], | |
477 | ['a', 'b', 'c', 'e']], |
|
499 | ['a', 'b', 'c', 'e']], | |
478 | dtype='|S1') |
|
500 | dtype='|S1') | |
479 |
|
501 | |||
480 | In [22]: %%R -d datar |
|
502 | In [22]: %%R -d datar | |
481 | datar = datapy |
|
503 | datar = datapy | |
482 | ....: |
|
504 | ....: | |
483 |
|
505 | |||
484 | In [23]: datar |
|
506 | In [23]: datar | |
485 | Out[23]: |
|
507 | Out[23]: | |
486 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
508 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
487 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
509 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
488 |
|
510 | |||
489 | The --dataframe argument first tries colnames, then names. |
|
511 | The --dataframe argument first tries colnames, then names. | |
490 | If both are NULL, it returns an ndarray (i.e. unstructured):: |
|
512 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
491 |
|
513 | |||
492 | In [1]: %R mydata=c(4,6,8.3); NULL |
|
514 | In [1]: %R mydata=c(4,6,8.3); NULL | |
493 |
|
515 | |||
494 | In [2]: %R -d mydata |
|
516 | In [2]: %R -d mydata | |
495 |
|
517 | |||
496 | In [3]: mydata |
|
518 | In [3]: mydata | |
497 | Out[3]: array([ 4. , 6. , 8.3]) |
|
519 | Out[3]: array([ 4. , 6. , 8.3]) | |
498 |
|
520 | |||
499 | In [4]: %R names(mydata) = c('a','b','c'); NULL |
|
521 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
500 |
|
522 | |||
501 | In [5]: %R -d mydata |
|
523 | In [5]: %R -d mydata | |
502 |
|
524 | |||
503 | In [6]: mydata |
|
525 | In [6]: mydata | |
504 | Out[6]: |
|
526 | Out[6]: | |
505 | array((4.0, 6.0, 8.3), |
|
527 | array((4.0, 6.0, 8.3), | |
506 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) |
|
528 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
507 |
|
529 | |||
508 | In [7]: %R -o mydata |
|
530 | In [7]: %R -o mydata | |
509 |
|
531 | |||
510 | In [8]: mydata |
|
532 | In [8]: mydata | |
511 | Out[8]: array([ 4. , 6. , 8.3]) |
|
533 | Out[8]: array([ 4. , 6. , 8.3]) | |
512 |
|
534 | |||
513 | ''' |
|
535 | ''' | |
514 |
|
536 | |||
515 | args = parse_argstring(self.R, line) |
|
537 | args = parse_argstring(self.R, line) | |
516 |
|
538 | |||
517 | # arguments 'code' in line are prepended to |
|
539 | # arguments 'code' in line are prepended to | |
518 | # the cell lines |
|
540 | # the cell lines | |
519 |
|
541 | |||
520 | if cell is None: |
|
542 | if cell is None: | |
521 | code = '' |
|
543 | code = '' | |
522 | return_output = True |
|
544 | return_output = True | |
523 | line_mode = True |
|
545 | line_mode = True | |
524 | else: |
|
546 | else: | |
525 | code = cell |
|
547 | code = cell | |
526 | return_output = False |
|
548 | return_output = False | |
527 | line_mode = False |
|
549 | line_mode = False | |
528 |
|
550 | |||
529 | code = ' '.join(args.code) + code |
|
551 | code = ' '.join(args.code) + code | |
530 |
|
552 | |||
531 | # if there is no local namespace then default to an empty dict |
|
553 | # if there is no local namespace then default to an empty dict | |
532 | if local_ns is None: |
|
554 | if local_ns is None: | |
533 | local_ns = {} |
|
555 | local_ns = {} | |
534 |
|
556 | |||
535 | if args.input: |
|
557 | if args.input: | |
536 | for input in ','.join(args.input).split(','): |
|
558 | for input in ','.join(args.input).split(','): | |
537 | try: |
|
559 | try: | |
538 | val = local_ns[input] |
|
560 | val = local_ns[input] | |
539 | except KeyError: |
|
561 | except KeyError: | |
540 | try: |
|
562 | try: | |
541 | val = self.shell.user_ns[input] |
|
563 | val = self.shell.user_ns[input] | |
542 | except KeyError: |
|
564 | except KeyError: | |
543 | raise NameError("name '%s' is not defined" % input) |
|
565 | raise NameError("name '%s' is not defined" % input) | |
544 | self.r.assign(input, self.pyconverter(val)) |
|
566 | self.r.assign(input, self.pyconverter(val)) | |
545 |
|
567 | |||
546 | if getattr(args, 'units') is not None: |
|
568 | if getattr(args, 'units') is not None: | |
547 | if args.units != "px" and getattr(args, 'res') is None: |
|
569 | if args.units != "px" and getattr(args, 'res') is None: | |
548 | args.res = 72 |
|
570 | args.res = 72 | |
549 | args.units = '"%s"' % args.units |
|
571 | args.units = '"%s"' % args.units | |
550 |
|
572 | |||
551 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) |
|
573 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |
552 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
574 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
553 | # execute the R code in a temporary directory |
|
575 | # execute the R code in a temporary directory | |
554 |
|
576 | |||
555 | tmpd = tempfile.mkdtemp() |
|
577 | tmpd = tempfile.mkdtemp() | |
556 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) |
|
578 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
557 |
|
579 | |||
558 | text_output = '' |
|
580 | text_output = '' | |
559 | if line_mode: |
|
581 | if line_mode: | |
560 | for line in code.split(';'): |
|
582 | for line in code.split(';'): | |
561 | text_result, result = self.eval(line) |
|
583 | text_result, result = self.eval(line) | |
562 | text_output += text_result |
|
584 | text_output += text_result | |
563 | if text_result: |
|
585 | if text_result: | |
564 | # the last line printed something to the console so we won't return it |
|
586 | # the last line printed something to the console so we won't return it | |
565 | return_output = False |
|
587 | return_output = False | |
566 | else: |
|
588 | else: | |
567 | text_result, result = self.eval(code) |
|
589 | text_result, result = self.eval(code) | |
568 | text_output += text_result |
|
590 | text_output += text_result | |
569 |
|
591 | |||
570 | self.r('dev.off()') |
|
592 | self.r('dev.off()') | |
571 |
|
593 | |||
572 | # read out all the saved .png files |
|
594 | # read out all the saved .png files | |
573 |
|
595 | |||
574 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
596 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
575 |
|
597 | |||
576 | # now publish the images |
|
598 | # now publish the images | |
577 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
599 | # mimicking IPython/zmq/pylab/backend_inline.py | |
578 | fmt = 'png' |
|
600 | fmt = 'png' | |
579 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
601 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
580 | mime = mimetypes[fmt] |
|
602 | mime = mimetypes[fmt] | |
581 |
|
603 | |||
582 | # publish the printed R objects, if any |
|
604 | # publish the printed R objects, if any | |
583 |
|
605 | |||
584 | display_data = [] |
|
606 | display_data = [] | |
585 | if text_output: |
|
607 | if text_output: | |
586 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
608 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
587 |
|
609 | |||
588 | # flush text streams before sending figures, helps a little with output |
|
610 | # flush text streams before sending figures, helps a little with output | |
589 | for image in images: |
|
611 | for image in images: | |
590 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
612 | # synchronization in the console (though it's a bandaid, not a real sln) | |
591 | sys.stdout.flush(); sys.stderr.flush() |
|
613 | sys.stdout.flush(); sys.stderr.flush() | |
592 | display_data.append(('RMagic.R', {mime: image})) |
|
614 | display_data.append(('RMagic.R', {mime: image})) | |
593 |
|
615 | |||
594 | # kill the temporary directory |
|
616 | # kill the temporary directory | |
595 | rmtree(tmpd) |
|
617 | rmtree(tmpd) | |
596 |
|
618 | |||
597 | # try to turn every output into a numpy array |
|
619 | # try to turn every output into a numpy array | |
598 | # this means that output are assumed to be castable |
|
620 | # this means that output are assumed to be castable | |
599 | # as numpy arrays |
|
621 | # as numpy arrays | |
600 |
|
622 | |||
601 | if args.output: |
|
623 | if args.output: | |
602 | for output in ','.join(args.output).split(','): |
|
624 | for output in ','.join(args.output).split(','): | |
603 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) |
|
625 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
604 |
|
626 | |||
605 | if args.dataframe: |
|
627 | if args.dataframe: | |
606 | for output in ','.join(args.dataframe).split(','): |
|
628 | for output in ','.join(args.dataframe).split(','): | |
607 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) |
|
629 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
608 |
|
630 | |||
609 | for tag, disp_d in display_data: |
|
631 | for tag, disp_d in display_data: | |
610 | publish_display_data(tag, disp_d) |
|
632 | publish_display_data(tag, disp_d) | |
611 |
|
633 | |||
612 | # this will keep a reference to the display_data |
|
634 | # this will keep a reference to the display_data | |
613 | # which might be useful to other objects who happen to use |
|
635 | # which might be useful to other objects who happen to use | |
614 | # this method |
|
636 | # this method | |
615 |
|
637 | |||
616 | if self.cache_display_data: |
|
638 | if self.cache_display_data: | |
617 | self.display_cache = display_data |
|
639 | self.display_cache = display_data | |
618 |
|
640 | |||
619 | # if in line mode and return_output, return the result as an ndarray |
|
641 | # if in line mode and return_output, return the result as an ndarray | |
620 | if return_output and not args.noreturn: |
|
642 | if return_output and not args.noreturn: | |
621 | if result != ri.NULL: |
|
643 | if result != ri.NULL: | |
622 | return self.Rconverter(result, dataframe=False) |
|
644 | return self.Rconverter(result, dataframe=False) | |
623 |
|
645 | |||
624 | __doc__ = __doc__.format( |
|
646 | __doc__ = __doc__.format( | |
625 | R_DOC = ' '*8 + RMagics.R.__doc__, |
|
647 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
626 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, |
|
648 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
627 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, |
|
649 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__, | |
628 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ |
|
650 | RGET_DOC = ' '*8 + RMagics.Rget.__doc__ | |
629 | ) |
|
651 | ) | |
630 |
|
652 | |||
631 |
|
653 | |||
632 | def load_ipython_extension(ip): |
|
654 | def load_ipython_extension(ip): | |
633 | """Load the extension in IPython.""" |
|
655 | """Load the extension in IPython.""" | |
634 | ip.register_magics(RMagics) |
|
656 | ip.register_magics(RMagics) | |
635 | # Initialising rpy2 interferes with readline. Since, at this point, we've |
|
657 | # Initialising rpy2 interferes with readline. Since, at this point, we've | |
636 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. |
|
658 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. | |
637 | if ip.has_readline: |
|
659 | if ip.has_readline: | |
638 | ip.readline.set_completer_delims(ip.readline_delims) |
|
660 | ip.readline.set_completer_delims(ip.readline_delims) |
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