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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 | .. note:: |
|
9 | .. note:: | |
10 |
|
10 | |||
11 | The ``rpy2`` package needs to be installed separately. It |
|
11 | The ``rpy2`` package needs to be installed separately. It | |
12 | can be obtained using ``easy_install`` or ``pip``. |
|
12 | can be obtained using ``easy_install`` or ``pip``. | |
13 |
|
13 | |||
14 | You will also need a working copy of R. |
|
14 | You will also need a working copy of R. | |
15 |
|
15 | |||
16 | Usage |
|
16 | Usage | |
17 | ===== |
|
17 | ===== | |
18 |
|
18 | |||
19 | To enable the magics below, execute ``%load_ext rmagic``. |
|
19 | To enable the magics below, execute ``%load_ext rmagic``. | |
20 |
|
20 | |||
21 | ``%R`` |
|
21 | ``%R`` | |
22 |
|
22 | |||
23 | {R_DOC} |
|
23 | {R_DOC} | |
24 |
|
24 | |||
25 | ``%Rpush`` |
|
25 | ``%Rpush`` | |
26 |
|
26 | |||
27 | {RPUSH_DOC} |
|
27 | {RPUSH_DOC} | |
28 |
|
28 | |||
29 | ``%Rpull`` |
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29 | ``%Rpull`` | |
30 |
|
30 | |||
31 | {RPULL_DOC} |
|
31 | {RPULL_DOC} | |
32 |
|
32 | |||
33 | ``%Rget`` |
|
33 | ``%Rget`` | |
34 |
|
34 | |||
35 | {RGET_DOC} |
|
35 | {RGET_DOC} | |
36 |
|
36 | |||
37 | """ |
|
37 | """ | |
38 | from __future__ import print_function |
|
38 | from __future__ import print_function | |
39 |
|
39 | |||
40 | #----------------------------------------------------------------------------- |
|
40 | #----------------------------------------------------------------------------- | |
41 | # Copyright (C) 2012 The IPython Development Team |
|
41 | # Copyright (C) 2012 The IPython Development Team | |
42 | # |
|
42 | # | |
43 | # Distributed under the terms of the BSD License. The full license is in |
|
43 | # Distributed under the terms of the BSD License. The full license is in | |
44 | # the file COPYING, distributed as part of this software. |
|
44 | # the file COPYING, distributed as part of this software. | |
45 | #----------------------------------------------------------------------------- |
|
45 | #----------------------------------------------------------------------------- | |
46 |
|
46 | |||
47 | import sys |
|
47 | import sys | |
48 | import tempfile |
|
48 | import tempfile | |
49 | from glob import glob |
|
49 | from glob import glob | |
50 | from shutil import rmtree |
|
50 | from shutil import rmtree | |
51 | import warnings |
|
51 | import warnings | |
52 |
|
52 | |||
53 | # numpy and rpy2 imports |
|
53 | # numpy and rpy2 imports | |
54 |
|
54 | |||
55 | import numpy as np |
|
55 | import numpy as np | |
56 |
|
56 | |||
57 | import rpy2.rinterface as ri |
|
57 | import rpy2.rinterface as ri | |
58 | import rpy2.robjects as ro |
|
58 | import rpy2.robjects as ro | |
59 | try: |
|
59 | try: | |
60 | from rpy2.robjects import pandas2ri |
|
60 | from rpy2.robjects import pandas2ri | |
61 | pandas2ri.activate() |
|
61 | pandas2ri.activate() | |
62 | except ImportError: |
|
62 | except ImportError: | |
63 | pandas2ri = None |
|
63 | pandas2ri = None | |
64 | from rpy2.robjects import numpy2ri |
|
64 | from rpy2.robjects import numpy2ri | |
65 | numpy2ri.activate() |
|
65 | numpy2ri.activate() | |
66 |
|
66 | |||
67 | # IPython imports |
|
67 | # IPython imports | |
68 |
|
68 | |||
69 | from IPython.core.displaypub import publish_display_data |
|
69 | from IPython.core.displaypub import publish_display_data | |
70 | from IPython.core.magic import (Magics, magics_class, line_magic, |
|
70 | from IPython.core.magic import (Magics, magics_class, line_magic, | |
71 | line_cell_magic, needs_local_scope) |
|
71 | line_cell_magic, needs_local_scope) | |
72 | from IPython.testing.skipdoctest import skip_doctest |
|
72 | from IPython.testing.skipdoctest import skip_doctest | |
73 | from IPython.core.magic_arguments import ( |
|
73 | from IPython.core.magic_arguments import ( | |
74 | argument, magic_arguments, parse_argstring |
|
74 | argument, magic_arguments, parse_argstring | |
75 | ) |
|
75 | ) | |
76 | from IPython.external.simplegeneric import generic |
|
76 | from IPython.external.simplegeneric import generic | |
77 | from IPython.utils.py3compat import (str_to_unicode, unicode_to_str, PY3, |
|
77 | from IPython.utils.py3compat import (str_to_unicode, unicode_to_str, PY3, | |
78 | unicode_type) |
|
78 | unicode_type) | |
79 | from IPython.utils.text import dedent |
|
79 | from IPython.utils.text import dedent | |
80 |
|
80 | |||
81 | class RInterpreterError(ri.RRuntimeError): |
|
81 | class RInterpreterError(ri.RRuntimeError): | |
82 | """An error when running R code in a %%R magic cell.""" |
|
82 | """An error when running R code in a %%R magic cell.""" | |
83 | def __init__(self, line, err, stdout): |
|
83 | def __init__(self, line, err, stdout): | |
84 | self.line = line |
|
84 | self.line = line | |
85 | self.err = err.rstrip() |
|
85 | self.err = err.rstrip() | |
86 | self.stdout = stdout.rstrip() |
|
86 | self.stdout = stdout.rstrip() | |
87 |
|
87 | |||
88 | def __unicode__(self): |
|
88 | def __unicode__(self): | |
89 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ |
|
89 | s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \ | |
90 | (self.line, self.err) |
|
90 | (self.line, self.err) | |
91 | if self.stdout and (self.stdout != self.err): |
|
91 | if self.stdout and (self.stdout != self.err): | |
92 | s += '\nR stdout:\n' + self.stdout |
|
92 | s += '\nR stdout:\n' + self.stdout | |
93 | return s |
|
93 | return s | |
94 |
|
94 | |||
95 | if PY3: |
|
95 | if PY3: | |
96 | __str__ = __unicode__ |
|
96 | __str__ = __unicode__ | |
97 | else: |
|
97 | else: | |
98 | def __str__(self): |
|
98 | def __str__(self): | |
99 | return unicode_to_str(unicode(self), 'utf-8') |
|
99 | return unicode_to_str(unicode(self), 'utf-8') | |
100 |
|
100 | |||
101 | def Rconverter(Robj, dataframe=False): |
|
101 | def Rconverter(Robj, dataframe=False): | |
102 | """ |
|
102 | """ | |
103 | Convert an object in R's namespace to one suitable |
|
103 | Convert an object in R's namespace to one suitable | |
104 | for ipython's namespace. |
|
104 | for ipython's namespace. | |
105 |
|
105 | |||
106 | For a data.frame, it tries to return a structured array. |
|
106 | For a data.frame, it tries to return a structured array. | |
107 | It first checks for colnames, then names. |
|
107 | It first checks for colnames, then names. | |
108 | If all are NULL, it returns np.asarray(Robj), else |
|
108 | If all are NULL, it returns np.asarray(Robj), else | |
109 | it tries to construct a recarray |
|
109 | it tries to construct a recarray | |
110 |
|
110 | |||
111 | Parameters |
|
111 | Parameters | |
112 | ---------- |
|
112 | ---------- | |
113 |
|
113 | |||
114 | Robj: an R object returned from rpy2 |
|
114 | Robj: an R object returned from rpy2 | |
115 | """ |
|
115 | """ | |
116 | is_data_frame = ro.r('is.data.frame') |
|
116 | is_data_frame = ro.r('is.data.frame') | |
117 | colnames = ro.r('colnames') |
|
117 | colnames = ro.r('colnames') | |
118 | rownames = ro.r('rownames') # with pandas, these could be used for the index |
|
118 | rownames = ro.r('rownames') # with pandas, these could be used for the index | |
119 | names = ro.r('names') |
|
119 | names = ro.r('names') | |
120 |
|
120 | |||
121 | if dataframe: |
|
121 | if dataframe: | |
122 | as_data_frame = ro.r('as.data.frame') |
|
122 | as_data_frame = ro.r('as.data.frame') | |
123 | cols = colnames(Robj) |
|
123 | cols = colnames(Robj) | |
124 | _names = names(Robj) |
|
124 | _names = names(Robj) | |
125 | if cols != ri.NULL: |
|
125 | if cols != ri.NULL: | |
126 | Robj = as_data_frame(Robj) |
|
126 | Robj = as_data_frame(Robj) | |
127 | names = tuple(np.array(cols)) |
|
127 | names = tuple(np.array(cols)) | |
128 | elif _names != ri.NULL: |
|
128 | elif _names != ri.NULL: | |
129 | names = tuple(np.array(_names)) |
|
129 | names = tuple(np.array(_names)) | |
130 | else: # failed to find names |
|
130 | else: # failed to find names | |
131 | return np.asarray(Robj) |
|
131 | return np.asarray(Robj) | |
132 | Robj = np.rec.fromarrays(Robj, names = names) |
|
132 | Robj = np.rec.fromarrays(Robj, names = names) | |
133 | return np.asarray(Robj) |
|
133 | return np.asarray(Robj) | |
134 |
|
134 | |||
135 | @generic |
|
135 | @generic | |
136 | def pyconverter(pyobj): |
|
136 | def pyconverter(pyobj): | |
137 | """Convert Python objects to R objects. Add types using the decorator: |
|
137 | """Convert Python objects to R objects. Add types using the decorator: | |
138 |
|
138 | |||
139 | @pyconverter.when_type |
|
139 | @pyconverter.when_type | |
140 | """ |
|
140 | """ | |
141 | return pyobj |
|
141 | return pyobj | |
142 |
|
142 | |||
143 | # The default conversion for lists seems to make them a nested list. That has |
|
143 | # The default conversion for lists seems to make them a nested list. That has | |
144 | # some advantages, but is rarely convenient, so for interactive use, we convert |
|
144 | # some advantages, but is rarely convenient, so for interactive use, we convert | |
145 | # lists to a numpy array, which becomes an R vector. |
|
145 | # lists to a numpy array, which becomes an R vector. | |
146 | @pyconverter.when_type(list) |
|
146 | @pyconverter.when_type(list) | |
147 | def pyconverter_list(pyobj): |
|
147 | def pyconverter_list(pyobj): | |
148 | return np.asarray(pyobj) |
|
148 | return np.asarray(pyobj) | |
149 |
|
149 | |||
150 | if pandas2ri is None: |
|
150 | if pandas2ri is None: | |
151 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' |
|
151 | # pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas' | |
152 | # conversion function. |
|
152 | # conversion function. | |
153 | try: |
|
153 | try: | |
154 | from pandas import DataFrame |
|
154 | from pandas import DataFrame | |
155 | from pandas.rpy.common import convert_to_r_dataframe |
|
155 | from pandas.rpy.common import convert_to_r_dataframe | |
156 | @pyconverter.when_type(DataFrame) |
|
156 | @pyconverter.when_type(DataFrame) | |
157 | def pyconverter_dataframe(pyobj): |
|
157 | def pyconverter_dataframe(pyobj): | |
158 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) |
|
158 | return convert_to_r_dataframe(pyobj, strings_as_factors=True) | |
159 | except ImportError: |
|
159 | except ImportError: | |
160 | pass |
|
160 | pass | |
161 |
|
161 | |||
162 | @magics_class |
|
162 | @magics_class | |
163 | class RMagics(Magics): |
|
163 | class RMagics(Magics): | |
164 | """A set of magics useful for interactive work with R via rpy2. |
|
164 | """A set of magics useful for interactive work with R via rpy2. | |
165 | """ |
|
165 | """ | |
166 |
|
166 | |||
167 | def __init__(self, shell, Rconverter=Rconverter, |
|
167 | def __init__(self, shell, Rconverter=Rconverter, | |
168 | pyconverter=pyconverter, |
|
168 | pyconverter=pyconverter, | |
169 | cache_display_data=False): |
|
169 | cache_display_data=False): | |
170 | """ |
|
170 | """ | |
171 | Parameters |
|
171 | Parameters | |
172 | ---------- |
|
172 | ---------- | |
173 |
|
173 | |||
174 | shell : IPython shell |
|
174 | shell : IPython shell | |
175 |
|
175 | |||
176 | Rconverter : callable |
|
176 | Rconverter : callable | |
177 | To be called on values taken from R before putting them in the |
|
177 | To be called on values taken from R before putting them in the | |
178 | IPython namespace. |
|
178 | IPython namespace. | |
179 |
|
179 | |||
180 | pyconverter : callable |
|
180 | pyconverter : callable | |
181 | To be called on values in ipython namespace before |
|
181 | To be called on values in ipython namespace before | |
182 | assigning to variables in rpy2. |
|
182 | assigning to variables in rpy2. | |
183 |
|
183 | |||
184 | cache_display_data : bool |
|
184 | cache_display_data : bool | |
185 | If True, the published results of the final call to R are |
|
185 | If True, the published results of the final call to R are | |
186 | cached in the variable 'display_cache'. |
|
186 | cached in the variable 'display_cache'. | |
187 |
|
187 | |||
188 | """ |
|
188 | """ | |
189 | super(RMagics, self).__init__(shell) |
|
189 | super(RMagics, self).__init__(shell) | |
190 | self.cache_display_data = cache_display_data |
|
190 | self.cache_display_data = cache_display_data | |
191 |
|
191 | |||
192 | self.r = ro.R() |
|
192 | self.r = ro.R() | |
193 |
|
193 | |||
194 | self.Rstdout_cache = [] |
|
194 | self.Rstdout_cache = [] | |
195 | self.pyconverter = pyconverter |
|
195 | self.pyconverter = pyconverter | |
196 | self.Rconverter = Rconverter |
|
196 | self.Rconverter = Rconverter | |
197 |
|
197 | |||
198 | def eval(self, line): |
|
198 | def eval(self, line): | |
199 | ''' |
|
199 | ''' | |
200 | Parse and evaluate a line of R code with rpy2. |
|
200 | Parse and evaluate a line of R code with rpy2. | |
201 | Returns the output to R's stdout() connection, |
|
201 | Returns the output to R's stdout() connection, | |
202 | the value generated by evaluating the code, and a |
|
202 | the value generated by evaluating the code, and a | |
203 | boolean indicating whether the return value would be |
|
203 | boolean indicating whether the return value would be | |
204 | visible if the line of code were evaluated in an R REPL. |
|
204 | visible if the line of code were evaluated in an R REPL. | |
205 |
|
205 | |||
206 | R Code evaluation and visibility determination are |
|
206 | R Code evaluation and visibility determination are | |
207 | done via an R call of the form withVisible({<code>}) |
|
207 | done via an R call of the form withVisible({<code>}) | |
208 |
|
208 | |||
209 | ''' |
|
209 | ''' | |
210 | old_writeconsole = ri.get_writeconsole() |
|
210 | old_writeconsole = ri.get_writeconsole() | |
211 | ri.set_writeconsole(self.write_console) |
|
211 | ri.set_writeconsole(self.write_console) | |
212 | try: |
|
212 | try: | |
213 | res = ro.r("withVisible({%s\n})" % line) |
|
213 | res = ro.r("withVisible({%s\n})" % line) | |
214 | value = res[0] #value (R object) |
|
214 | value = res[0] #value (R object) | |
215 | visible = ro.conversion.ri2py(res[1])[0] #visible (boolean) |
|
215 | visible = ro.conversion.ri2py(res[1])[0] #visible (boolean) | |
216 | except (ri.RRuntimeError, ValueError) as exception: |
|
216 | except (ri.RRuntimeError, ValueError) as exception: | |
217 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error |
|
217 | warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error | |
218 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) |
|
218 | raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg) | |
219 | text_output = self.flush() |
|
219 | text_output = self.flush() | |
220 | ri.set_writeconsole(old_writeconsole) |
|
220 | ri.set_writeconsole(old_writeconsole) | |
221 | return text_output, value, visible |
|
221 | return text_output, value, visible | |
222 |
|
222 | |||
223 | def write_console(self, output): |
|
223 | def write_console(self, output): | |
224 | ''' |
|
224 | ''' | |
225 | A hook to capture R's stdout in a cache. |
|
225 | A hook to capture R's stdout in a cache. | |
226 | ''' |
|
226 | ''' | |
227 | self.Rstdout_cache.append(output) |
|
227 | self.Rstdout_cache.append(output) | |
228 |
|
228 | |||
229 | def flush(self): |
|
229 | def flush(self): | |
230 | ''' |
|
230 | ''' | |
231 | Flush R's stdout cache to a string, returning the string. |
|
231 | Flush R's stdout cache to a string, returning the string. | |
232 | ''' |
|
232 | ''' | |
233 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
233 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
234 | self.Rstdout_cache = [] |
|
234 | self.Rstdout_cache = [] | |
235 | return value |
|
235 | return value | |
236 |
|
236 | |||
237 | @skip_doctest |
|
237 | @skip_doctest | |
238 | @needs_local_scope |
|
238 | @needs_local_scope | |
239 | @line_magic |
|
239 | @line_magic | |
240 | def Rpush(self, line, local_ns=None): |
|
240 | def Rpush(self, line, local_ns=None): | |
241 | ''' |
|
241 | ''' | |
242 | A line-level magic for R that pushes |
|
242 | A line-level magic for R that pushes | |
243 | variables from python to rpy2. The line should be made up |
|
243 | variables from python to rpy2. The line should be made up | |
244 | of whitespace separated variable names in the IPython |
|
244 | of whitespace separated variable names in the IPython | |
245 | namespace:: |
|
245 | namespace:: | |
246 |
|
246 | |||
247 | In [7]: import numpy as np |
|
247 | In [7]: import numpy as np | |
248 |
|
248 | |||
249 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
249 | In [8]: X = np.array([4.5,6.3,7.9]) | |
250 |
|
250 | |||
251 | In [9]: X.mean() |
|
251 | In [9]: X.mean() | |
252 | Out[9]: 6.2333333333333343 |
|
252 | Out[9]: 6.2333333333333343 | |
253 |
|
253 | |||
254 | In [10]: %Rpush X |
|
254 | In [10]: %Rpush X | |
255 |
|
255 | |||
256 | In [11]: %R mean(X) |
|
256 | In [11]: %R mean(X) | |
257 | Out[11]: array([ 6.23333333]) |
|
257 | Out[11]: array([ 6.23333333]) | |
258 |
|
258 | |||
259 | ''' |
|
259 | ''' | |
260 | if local_ns is None: |
|
260 | if local_ns is None: | |
261 | local_ns = {} |
|
261 | local_ns = {} | |
262 |
|
262 | |||
263 | inputs = line.split(' ') |
|
263 | inputs = line.split(' ') | |
264 | for input in inputs: |
|
264 | for input in inputs: | |
265 | try: |
|
265 | try: | |
266 | val = local_ns[input] |
|
266 | val = local_ns[input] | |
267 | except KeyError: |
|
267 | except KeyError: | |
268 | try: |
|
268 | try: | |
269 | val = self.shell.user_ns[input] |
|
269 | val = self.shell.user_ns[input] | |
270 | except KeyError: |
|
270 | except KeyError: | |
271 | # reraise the KeyError as a NameError so that it looks like |
|
271 | # reraise the KeyError as a NameError so that it looks like | |
272 | # the standard python behavior when you use an unnamed |
|
272 | # the standard python behavior when you use an unnamed | |
273 | # variable |
|
273 | # variable | |
274 | raise NameError("name '%s' is not defined" % input) |
|
274 | raise NameError("name '%s' is not defined" % input) | |
275 |
|
275 | |||
276 | self.r.assign(input, self.pyconverter(val)) |
|
276 | self.r.assign(input, self.pyconverter(val)) | |
277 |
|
277 | |||
278 | @skip_doctest |
|
278 | @skip_doctest | |
279 | @magic_arguments() |
|
279 | @magic_arguments() | |
280 | @argument( |
|
280 | @argument( | |
281 | '-d', '--as_dataframe', action='store_true', |
|
281 | '-d', '--as_dataframe', action='store_true', | |
282 | default=False, |
|
282 | default=False, | |
283 | help='Convert objects to data.frames before returning to ipython.' |
|
283 | help='Convert objects to data.frames before returning to ipython.' | |
284 | ) |
|
284 | ) | |
285 | @argument( |
|
285 | @argument( | |
286 | 'outputs', |
|
286 | 'outputs', | |
287 | nargs='*', |
|
287 | nargs='*', | |
288 | ) |
|
288 | ) | |
289 | @line_magic |
|
289 | @line_magic | |
290 | def Rpull(self, line): |
|
290 | def Rpull(self, line): | |
291 | ''' |
|
291 | ''' | |
292 | A line-level magic for R that pulls |
|
292 | A line-level magic for R that pulls | |
293 | variables from python to rpy2:: |
|
293 | variables from python to rpy2:: | |
294 |
|
294 | |||
295 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
295 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
296 |
|
296 | |||
297 | In [19]: %Rpull x y z |
|
297 | In [19]: %Rpull x y z | |
298 |
|
298 | |||
299 | In [20]: x |
|
299 | In [20]: x | |
300 | Out[20]: array([ 3. , 4. , 6.7]) |
|
300 | Out[20]: array([ 3. , 4. , 6.7]) | |
301 |
|
301 | |||
302 | In [21]: y |
|
302 | In [21]: y | |
303 | Out[21]: array([ 4., 6., 7.]) |
|
303 | Out[21]: array([ 4., 6., 7.]) | |
304 |
|
304 | |||
305 | In [22]: z |
|
305 | In [22]: z | |
306 | Out[22]: |
|
306 | Out[22]: | |
307 | array(['a', '3', '4'], |
|
307 | array(['a', '3', '4'], | |
308 | dtype='|S1') |
|
308 | dtype='|S1') | |
309 |
|
309 | |||
310 |
|
310 | |||
311 | If --as_dataframe, then each object is returned as a structured array |
|
311 | If --as_dataframe, then each object is returned as a structured array | |
312 | after first passed through "as.data.frame" in R before |
|
312 | after first passed through "as.data.frame" in R before | |
313 | being calling self.Rconverter. |
|
313 | being calling self.Rconverter. | |
314 | This is useful when a structured array is desired as output, or |
|
314 | This is useful when a structured array is desired as output, or | |
315 | when the object in R has mixed data types. |
|
315 | when the object in R has mixed data types. | |
316 | See the %%R docstring for more examples. |
|
316 | See the %%R docstring for more examples. | |
317 |
|
317 | |||
318 | Notes |
|
318 | Notes | |
319 | ----- |
|
319 | ----- | |
320 |
|
320 | |||
321 | Beware that R names can have '.' so this is not fool proof. |
|
321 | Beware that R names can have '.' so this is not fool proof. | |
322 | To avoid this, don't name your R objects with '.'s... |
|
322 | To avoid this, don't name your R objects with '.'s... | |
323 |
|
323 | |||
324 | ''' |
|
324 | ''' | |
325 | args = parse_argstring(self.Rpull, line) |
|
325 | args = parse_argstring(self.Rpull, line) | |
326 | outputs = args.outputs |
|
326 | outputs = args.outputs | |
327 | for output in outputs: |
|
327 | for output in outputs: | |
328 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) |
|
328 | self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)}) | |
329 |
|
329 | |||
330 | @skip_doctest |
|
330 | @skip_doctest | |
331 | @magic_arguments() |
|
331 | @magic_arguments() | |
332 | @argument( |
|
332 | @argument( | |
333 | '-d', '--as_dataframe', action='store_true', |
|
333 | '-d', '--as_dataframe', action='store_true', | |
334 | default=False, |
|
334 | default=False, | |
335 | help='Convert objects to data.frames before returning to ipython.' |
|
335 | help='Convert objects to data.frames before returning to ipython.' | |
336 | ) |
|
336 | ) | |
337 | @argument( |
|
337 | @argument( | |
338 | 'output', |
|
338 | 'output', | |
339 | nargs=1, |
|
339 | nargs=1, | |
340 | type=str, |
|
340 | type=str, | |
341 | ) |
|
341 | ) | |
342 | @line_magic |
|
342 | @line_magic | |
343 | def Rget(self, line): |
|
343 | def Rget(self, line): | |
344 | ''' |
|
344 | ''' | |
345 | Return an object from rpy2, possibly as a structured array (if possible). |
|
345 | Return an object from rpy2, possibly as a structured array (if possible). | |
346 | Similar to Rpull except only one argument is accepted and the value is |
|
346 | Similar to Rpull except only one argument is accepted and the value is | |
347 | returned rather than pushed to self.shell.user_ns:: |
|
347 | returned rather than pushed to self.shell.user_ns:: | |
348 |
|
348 | |||
349 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
349 | In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
350 |
|
350 | |||
351 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
351 | In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
352 |
|
352 | |||
353 | In [5]: %R -i datapy |
|
353 | In [5]: %R -i datapy | |
354 |
|
354 | |||
355 | In [6]: %Rget datapy |
|
355 | In [6]: %Rget datapy | |
356 | Out[6]: |
|
356 | Out[6]: | |
357 | array([['1', '2', '3', '4'], |
|
357 | array([['1', '2', '3', '4'], | |
358 | ['2', '3', '2', '5'], |
|
358 | ['2', '3', '2', '5'], | |
359 | ['a', 'b', 'c', 'e']], |
|
359 | ['a', 'b', 'c', 'e']], | |
360 | dtype='|S1') |
|
360 | dtype='|S1') | |
361 |
|
361 | |||
362 | In [7]: %Rget -d datapy |
|
362 | In [7]: %Rget -d datapy | |
363 | Out[7]: |
|
363 | Out[7]: | |
364 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
364 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
365 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
365 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
366 |
|
366 | |||
367 | ''' |
|
367 | ''' | |
368 | args = parse_argstring(self.Rget, line) |
|
368 | args = parse_argstring(self.Rget, line) | |
369 | output = args.output |
|
369 | output = args.output | |
370 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) |
|
370 | return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe) | |
371 |
|
371 | |||
372 |
|
372 | |||
373 | @skip_doctest |
|
373 | @skip_doctest | |
374 | @magic_arguments() |
|
374 | @magic_arguments() | |
375 | @argument( |
|
375 | @argument( | |
376 | '-i', '--input', action='append', |
|
376 | '-i', '--input', action='append', | |
377 | 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.' |
|
377 | 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.' | |
378 | ) |
|
378 | ) | |
379 | @argument( |
|
379 | @argument( | |
380 | '-o', '--output', action='append', |
|
380 | '-o', '--output', action='append', | |
381 | 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.' |
|
381 | 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.' | |
382 | ) |
|
382 | ) | |
383 | @argument( |
|
383 | @argument( | |
384 | '-w', '--width', type=int, |
|
384 | '-w', '--width', type=int, | |
385 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
385 | help='Width of png plotting device sent as an argument to *png* in R.' | |
386 | ) |
|
386 | ) | |
387 | @argument( |
|
387 | @argument( | |
388 | '-h', '--height', type=int, |
|
388 | '-h', '--height', type=int, | |
389 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
389 | help='Height of png plotting device sent as an argument to *png* in R.' | |
390 | ) |
|
390 | ) | |
391 |
|
391 | |||
392 | @argument( |
|
392 | @argument( | |
393 | '-d', '--dataframe', action='append', |
|
393 | '-d', '--dataframe', action='append', | |
394 | help='Convert these objects to data.frames and return as structured arrays.' |
|
394 | help='Convert these objects to data.frames and return as structured arrays.' | |
395 | ) |
|
395 | ) | |
396 | @argument( |
|
396 | @argument( | |
397 | '-u', '--units', type=unicode_type, choices=["px", "in", "cm", "mm"], |
|
397 | '-u', '--units', type=unicode_type, choices=["px", "in", "cm", "mm"], | |
398 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
398 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
399 | ) |
|
399 | ) | |
400 | @argument( |
|
400 | @argument( | |
401 | '-r', '--res', type=int, |
|
401 | '-r', '--res', type=int, | |
402 | 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"].' |
|
402 | 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"].' | |
403 | ) |
|
403 | ) | |
404 | @argument( |
|
404 | @argument( | |
405 | '-p', '--pointsize', type=int, |
|
405 | '-p', '--pointsize', type=int, | |
406 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
406 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
407 | ) |
|
407 | ) | |
408 | @argument( |
|
408 | @argument( | |
409 | '-b', '--bg', |
|
409 | '-b', '--bg', | |
410 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
410 | help='Background of png plotting device sent as an argument to *png* in R.' | |
411 | ) |
|
411 | ) | |
412 | @argument( |
|
412 | @argument( | |
413 | '-n', '--noreturn', |
|
413 | '-n', '--noreturn', | |
414 | help='Force the magic to not return anything.', |
|
414 | help='Force the magic to not return anything.', | |
415 | action='store_true', |
|
415 | action='store_true', | |
416 | default=False |
|
416 | default=False | |
417 | ) |
|
417 | ) | |
418 | @argument( |
|
418 | @argument( | |
419 | 'code', |
|
419 | 'code', | |
420 | nargs='*', |
|
420 | nargs='*', | |
421 | ) |
|
421 | ) | |
422 | @needs_local_scope |
|
422 | @needs_local_scope | |
423 | @line_cell_magic |
|
423 | @line_cell_magic | |
424 | def R(self, line, cell=None, local_ns=None): |
|
424 | def R(self, line, cell=None, local_ns=None): | |
425 | ''' |
|
425 | ''' | |
426 | Execute code in R, and pull some of the results back into the Python namespace. |
|
426 | Execute code in R, and pull some of the results back into the Python namespace. | |
427 |
|
427 | |||
428 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
428 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
429 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
429 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
430 | final line. |
|
430 | final line. | |
431 |
|
431 | |||
432 | Multiple R lines can be executed by joining them with semicolons:: |
|
432 | Multiple R lines can be executed by joining them with semicolons:: | |
433 |
|
433 | |||
434 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
434 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
435 | Out[9]: array([ 4.25]) |
|
435 | Out[9]: array([ 4.25]) | |
436 |
|
436 | |||
437 | In cell mode, this will run a block of R code. The resulting value |
|
437 | In cell mode, this will run a block of R code. The resulting value | |
438 | is printed if it would printed be when evaluating the same code |
|
438 | is printed if it would printed be when evaluating the same code | |
439 | within a standard R REPL. |
|
439 | within a standard R REPL. | |
440 |
|
440 | |||
441 | Nothing is returned to python by default in cell mode:: |
|
441 | Nothing is returned to python by default in cell mode:: | |
442 |
|
442 | |||
443 | In [10]: %%R |
|
443 | In [10]: %%R | |
444 | ....: Y = c(2,4,3,9) |
|
444 | ....: Y = c(2,4,3,9) | |
445 | ....: summary(lm(Y~X)) |
|
445 | ....: summary(lm(Y~X)) | |
446 |
|
446 | |||
447 | Call: |
|
447 | Call: | |
448 | lm(formula = Y ~ X) |
|
448 | lm(formula = Y ~ X) | |
449 |
|
449 | |||
450 | Residuals: |
|
450 | Residuals: | |
451 | 1 2 3 4 |
|
451 | 1 2 3 4 | |
452 | 0.88 -0.24 -2.28 1.64 |
|
452 | 0.88 -0.24 -2.28 1.64 | |
453 |
|
453 | |||
454 | Coefficients: |
|
454 | Coefficients: | |
455 | Estimate Std. Error t value Pr(>|t|) |
|
455 | Estimate Std. Error t value Pr(>|t|) | |
456 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
456 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
457 | X 1.0400 0.4822 2.157 0.164 |
|
457 | X 1.0400 0.4822 2.157 0.164 | |
458 |
|
458 | |||
459 | Residual standard error: 2.088 on 2 degrees of freedom |
|
459 | Residual standard error: 2.088 on 2 degrees of freedom | |
460 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
460 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
461 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
461 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
462 |
|
462 | |||
463 | In the notebook, plots are published as the output of the cell:: |
|
463 | In the notebook, plots are published as the output of the cell:: | |
464 |
|
464 | |||
465 | %R plot(X, Y) |
|
465 | %R plot(X, Y) | |
466 |
|
466 | |||
467 | will create a scatter plot of X bs Y. |
|
467 | will create a scatter plot of X bs Y. | |
468 |
|
468 | |||
469 | If cell is not None and line has some R code, it is prepended to |
|
469 | If cell is not None and line has some R code, it is prepended to | |
470 | the R code in cell. |
|
470 | the R code in cell. | |
471 |
|
471 | |||
472 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
472 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
473 |
|
473 | |||
474 | In [14]: Z = np.array([1,4,5,10]) |
|
474 | In [14]: Z = np.array([1,4,5,10]) | |
475 |
|
475 | |||
476 | In [15]: %R -i Z mean(Z) |
|
476 | In [15]: %R -i Z mean(Z) | |
477 | Out[15]: array([ 5.]) |
|
477 | Out[15]: array([ 5.]) | |
478 |
|
478 | |||
479 |
|
479 | |||
480 | In [16]: %R -o W W=Z*mean(Z) |
|
480 | In [16]: %R -o W W=Z*mean(Z) | |
481 | Out[16]: array([ 5., 20., 25., 50.]) |
|
481 | Out[16]: array([ 5., 20., 25., 50.]) | |
482 |
|
482 | |||
483 | In [17]: W |
|
483 | In [17]: W | |
484 | Out[17]: array([ 5., 20., 25., 50.]) |
|
484 | Out[17]: array([ 5., 20., 25., 50.]) | |
485 |
|
485 | |||
486 | The return value is determined by these rules: |
|
486 | The return value is determined by these rules: | |
487 |
|
487 | |||
488 | * If the cell is not None, the magic returns None. |
|
488 | * If the cell is not None, the magic returns None. | |
489 |
|
489 | |||
490 | * If the cell evaluates as False, the resulting value is returned |
|
490 | * If the cell evaluates as False, the resulting value is returned | |
491 | unless the final line prints something to the console, in |
|
491 | unless the final line prints something to the console, in | |
492 | which case None is returned. |
|
492 | which case None is returned. | |
493 |
|
493 | |||
494 | * If the final line results in a NULL value when evaluated |
|
494 | * If the final line results in a NULL value when evaluated | |
495 | by rpy2, then None is returned. |
|
495 | by rpy2, then None is returned. | |
496 |
|
496 | |||
497 | * No attempt is made to convert the final value to a structured array. |
|
497 | * No attempt is made to convert the final value to a structured array. | |
498 | Use the --dataframe flag or %Rget to push / return a structured array. |
|
498 | Use the --dataframe flag or %Rget to push / return a structured array. | |
499 |
|
499 | |||
500 | * If the -n flag is present, there is no return value. |
|
500 | * If the -n flag is present, there is no return value. | |
501 |
|
501 | |||
502 | * A trailing ';' will also result in no return value as the last |
|
502 | * A trailing ';' will also result in no return value as the last | |
503 | value in the line is an empty string. |
|
503 | value in the line is an empty string. | |
504 |
|
504 | |||
505 | The --dataframe argument will attempt to return structured arrays. |
|
505 | The --dataframe argument will attempt to return structured arrays. | |
506 | This is useful for dataframes with |
|
506 | This is useful for dataframes with | |
507 | mixed data types. Note also that for a data.frame, |
|
507 | mixed data types. Note also that for a data.frame, | |
508 | if it is returned as an ndarray, it is transposed:: |
|
508 | if it is returned as an ndarray, it is transposed:: | |
509 |
|
509 | |||
510 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] |
|
510 | In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')] | |
511 |
|
511 | |||
512 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) |
|
512 | In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype) | |
513 |
|
513 | |||
514 | In [20]: %%R -o datar |
|
514 | In [20]: %%R -o datar | |
515 | datar = datapy |
|
515 | datar = datapy | |
516 | ....: |
|
516 | ....: | |
517 |
|
517 | |||
518 | In [21]: datar |
|
518 | In [21]: datar | |
519 | Out[21]: |
|
519 | Out[21]: | |
520 | array([['1', '2', '3', '4'], |
|
520 | array([['1', '2', '3', '4'], | |
521 | ['2', '3', '2', '5'], |
|
521 | ['2', '3', '2', '5'], | |
522 | ['a', 'b', 'c', 'e']], |
|
522 | ['a', 'b', 'c', 'e']], | |
523 | dtype='|S1') |
|
523 | dtype='|S1') | |
524 |
|
524 | |||
525 | In [22]: %%R -d datar |
|
525 | In [22]: %%R -d datar | |
526 | datar = datapy |
|
526 | datar = datapy | |
527 | ....: |
|
527 | ....: | |
528 |
|
528 | |||
529 | In [23]: datar |
|
529 | In [23]: datar | |
530 | Out[23]: |
|
530 | Out[23]: | |
531 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], |
|
531 | array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')], | |
532 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) |
|
532 | dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]) | |
533 |
|
533 | |||
534 | The --dataframe argument first tries colnames, then names. |
|
534 | The --dataframe argument first tries colnames, then names. | |
535 | If both are NULL, it returns an ndarray (i.e. unstructured):: |
|
535 | If both are NULL, it returns an ndarray (i.e. unstructured):: | |
536 |
|
536 | |||
537 | In [1]: %R mydata=c(4,6,8.3); NULL |
|
537 | In [1]: %R mydata=c(4,6,8.3); NULL | |
538 |
|
538 | |||
539 | In [2]: %R -d mydata |
|
539 | In [2]: %R -d mydata | |
540 |
|
540 | |||
541 | In [3]: mydata |
|
541 | In [3]: mydata | |
542 | Out[3]: array([ 4. , 6. , 8.3]) |
|
542 | Out[3]: array([ 4. , 6. , 8.3]) | |
543 |
|
543 | |||
544 | In [4]: %R names(mydata) = c('a','b','c'); NULL |
|
544 | In [4]: %R names(mydata) = c('a','b','c'); NULL | |
545 |
|
545 | |||
546 | In [5]: %R -d mydata |
|
546 | In [5]: %R -d mydata | |
547 |
|
547 | |||
548 | In [6]: mydata |
|
548 | In [6]: mydata | |
549 | Out[6]: |
|
549 | Out[6]: | |
550 | array((4.0, 6.0, 8.3), |
|
550 | array((4.0, 6.0, 8.3), | |
551 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) |
|
551 | dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')]) | |
552 |
|
552 | |||
553 | In [7]: %R -o mydata |
|
553 | In [7]: %R -o mydata | |
554 |
|
554 | |||
555 | In [8]: mydata |
|
555 | In [8]: mydata | |
556 | Out[8]: array([ 4. , 6. , 8.3]) |
|
556 | Out[8]: array([ 4. , 6. , 8.3]) | |
557 |
|
557 | |||
558 | ''' |
|
558 | ''' | |
559 |
|
559 | |||
560 | args = parse_argstring(self.R, line) |
|
560 | args = parse_argstring(self.R, line) | |
561 |
|
561 | |||
562 | # arguments 'code' in line are prepended to |
|
562 | # arguments 'code' in line are prepended to | |
563 | # the cell lines |
|
563 | # the cell lines | |
564 |
|
564 | |||
565 | if cell is None: |
|
565 | if cell is None: | |
566 | code = '' |
|
566 | code = '' | |
567 | return_output = True |
|
567 | return_output = True | |
568 | line_mode = True |
|
568 | line_mode = True | |
569 | else: |
|
569 | else: | |
570 | code = cell |
|
570 | code = cell | |
571 | return_output = False |
|
571 | return_output = False | |
572 | line_mode = False |
|
572 | line_mode = False | |
573 |
|
573 | |||
574 | code = ' '.join(args.code) + code |
|
574 | code = ' '.join(args.code) + code | |
575 |
|
575 | |||
576 | # if there is no local namespace then default to an empty dict |
|
576 | # if there is no local namespace then default to an empty dict | |
577 | if local_ns is None: |
|
577 | if local_ns is None: | |
578 | local_ns = {} |
|
578 | local_ns = {} | |
579 |
|
579 | |||
580 | if args.input: |
|
580 | if args.input: | |
581 | for input in ','.join(args.input).split(','): |
|
581 | for input in ','.join(args.input).split(','): | |
582 | try: |
|
582 | try: | |
583 | val = local_ns[input] |
|
583 | val = local_ns[input] | |
584 | except KeyError: |
|
584 | except KeyError: | |
585 | try: |
|
585 | try: | |
586 | val = self.shell.user_ns[input] |
|
586 | val = self.shell.user_ns[input] | |
587 | except KeyError: |
|
587 | except KeyError: | |
588 | raise NameError("name '%s' is not defined" % input) |
|
588 | raise NameError("name '%s' is not defined" % input) | |
589 | self.r.assign(input, self.pyconverter(val)) |
|
589 | self.r.assign(input, self.pyconverter(val)) | |
590 |
|
590 | |||
591 | if getattr(args, 'units') is not None: |
|
591 | if getattr(args, 'units') is not None: | |
592 | if args.units != "px" and getattr(args, 'res') is None: |
|
592 | if args.units != "px" and getattr(args, 'res') is None: | |
593 | args.res = 72 |
|
593 | args.res = 72 | |
594 | args.units = '"%s"' % args.units |
|
594 | args.units = '"%s"' % args.units | |
595 |
|
595 | |||
596 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) |
|
596 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']]) | |
597 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
597 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
598 | # execute the R code in a temporary directory |
|
598 | # execute the R code in a temporary directory | |
599 |
|
599 | |||
600 | tmpd = tempfile.mkdtemp() |
|
600 | tmpd = tempfile.mkdtemp() | |
601 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) |
|
601 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) | |
602 |
|
602 | |||
603 | text_output = '' |
|
603 | text_output = '' | |
604 | try: |
|
604 | try: | |
605 | if line_mode: |
|
605 | if line_mode: | |
606 | for line in code.split(';'): |
|
606 | for line in code.split(';'): | |
607 | text_result, result, visible = self.eval(line) |
|
607 | text_result, result, visible = self.eval(line) | |
608 | text_output += text_result |
|
608 | text_output += text_result | |
609 | if text_result: |
|
609 | if text_result: | |
610 | # the last line printed something to the console so we won't return it |
|
610 | # the last line printed something to the console so we won't return it | |
611 | return_output = False |
|
611 | return_output = False | |
612 | else: |
|
612 | else: | |
613 | text_result, result, visible = self.eval(code) |
|
613 | text_result, result, visible = self.eval(code) | |
614 | text_output += text_result |
|
614 | text_output += text_result | |
615 | if visible: |
|
615 | if visible: | |
616 | old_writeconsole = ri.get_writeconsole() |
|
616 | old_writeconsole = ri.get_writeconsole() | |
617 | ri.set_writeconsole(self.write_console) |
|
617 | ri.set_writeconsole(self.write_console) | |
618 | ro.r.show(result) |
|
618 | ro.r.show(result) | |
619 | text_output += self.flush() |
|
619 | text_output += self.flush() | |
620 | ri.set_writeconsole(old_writeconsole) |
|
620 | ri.set_writeconsole(old_writeconsole) | |
621 |
|
621 | |||
622 | except RInterpreterError as e: |
|
622 | except RInterpreterError as e: | |
623 | print(e.stdout) |
|
623 | print(e.stdout) | |
624 | if not e.stdout.endswith(e.err): |
|
624 | if not e.stdout.endswith(e.err): | |
625 | print(e.err) |
|
625 | print(e.err) | |
626 | rmtree(tmpd) |
|
626 | rmtree(tmpd) | |
627 | return |
|
627 | return | |
628 | finally: |
|
628 | finally: | |
629 | self.r('dev.off()') |
|
629 | self.r('dev.off()') | |
630 |
|
630 | |||
631 | # read out all the saved .png files |
|
631 | # read out all the saved .png files | |
632 |
|
632 | |||
633 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
633 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
634 |
|
634 | |||
635 | # now publish the images |
|
635 | # now publish the images | |
636 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
636 | # mimicking IPython/zmq/pylab/backend_inline.py | |
637 | fmt = 'png' |
|
637 | fmt = 'png' | |
638 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
638 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
639 | mime = mimetypes[fmt] |
|
639 | mime = mimetypes[fmt] | |
640 |
|
640 | |||
641 | # publish the printed R objects, if any |
|
641 | # publish the printed R objects, if any | |
642 |
|
642 | |||
643 | display_data = [] |
|
643 | display_data = [] | |
644 | if text_output: |
|
644 | if text_output: | |
645 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
645 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
646 |
|
646 | |||
647 | # flush text streams before sending figures, helps a little with output |
|
647 | # flush text streams before sending figures, helps a little with output | |
648 | for image in images: |
|
648 | for image in images: | |
649 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
649 | # synchronization in the console (though it's a bandaid, not a real sln) | |
650 | sys.stdout.flush(); sys.stderr.flush() |
|
650 | sys.stdout.flush(); sys.stderr.flush() | |
651 | display_data.append(('RMagic.R', {mime: image})) |
|
651 | display_data.append(('RMagic.R', {mime: image})) | |
652 |
|
652 | |||
653 | # kill the temporary directory |
|
653 | # kill the temporary directory | |
654 | rmtree(tmpd) |
|
654 | rmtree(tmpd) | |
655 |
|
655 | |||
656 | # try to turn every output into a numpy array |
|
656 | # try to turn every output into a numpy array | |
657 | # this means that output are assumed to be castable |
|
657 | # this means that output are assumed to be castable | |
658 | # as numpy arrays |
|
658 | # as numpy arrays | |
659 |
|
659 | |||
660 | if args.output: |
|
660 | if args.output: | |
661 | for output in ','.join(args.output).split(','): |
|
661 | for output in ','.join(args.output).split(','): | |
662 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) |
|
662 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)}) | |
663 |
|
663 | |||
664 | if args.dataframe: |
|
664 | if args.dataframe: | |
665 | for output in ','.join(args.dataframe).split(','): |
|
665 | for output in ','.join(args.dataframe).split(','): | |
666 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) |
|
666 | self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)}) | |
667 |
|
667 | |||
668 | for tag, disp_d in display_data: |
|
668 | for tag, disp_d in display_data: | |
669 | publish_display_data(data=disp_d, source=tag) |
|
669 | publish_display_data(data=disp_d, source=tag) | |
670 |
|
670 | |||
671 | # this will keep a reference to the display_data |
|
671 | # this will keep a reference to the display_data | |
672 | # which might be useful to other objects who happen to use |
|
672 | # which might be useful to other objects who happen to use | |
673 | # this method |
|
673 | # this method | |
674 |
|
674 | |||
675 | if self.cache_display_data: |
|
675 | if self.cache_display_data: | |
676 | self.display_cache = display_data |
|
676 | self.display_cache = display_data | |
677 |
|
677 | |||
678 | # if in line mode and return_output, return the result as an ndarray |
|
678 | # if in line mode and return_output, return the result as an ndarray | |
679 | if return_output and not args.noreturn: |
|
679 | if return_output and not args.noreturn: | |
680 | if result != ri.NULL: |
|
680 | if result != ri.NULL: | |
681 | return self.Rconverter(result, dataframe=False) |
|
681 | return self.Rconverter(result, dataframe=False) | |
682 |
|
682 | |||
683 | __doc__ = __doc__.format( |
|
683 | __doc__ = __doc__.format( | |
684 | R_DOC = dedent(RMagics.R.__doc__), |
|
684 | R_DOC = dedent(RMagics.R.__doc__), | |
685 | RPUSH_DOC = dedent(RMagics.Rpush.__doc__), |
|
685 | RPUSH_DOC = dedent(RMagics.Rpush.__doc__), | |
686 | RPULL_DOC = dedent(RMagics.Rpull.__doc__), |
|
686 | RPULL_DOC = dedent(RMagics.Rpull.__doc__), | |
687 | RGET_DOC = dedent(RMagics.Rget.__doc__) |
|
687 | RGET_DOC = dedent(RMagics.Rget.__doc__) | |
688 | ) |
|
688 | ) | |
689 |
|
689 | |||
690 |
|
690 | |||
691 | def load_ipython_extension(ip): |
|
691 | def load_ipython_extension(ip): | |
692 | """Load the extension in IPython.""" |
|
692 | """Load the extension in IPython.""" | |
693 | warnings.warn("The rmagic extension in IPython is deprecated in favour of " |
|
693 | warnings.warn("The rmagic extension in IPython is deprecated in favour of " | |
694 |
"rpy2.ipython. If available, that will be loaded instead." |
|
694 | "rpy2.ipython. If available, that will be loaded instead.\n" | |
|
695 | "http://rpy.sourceforge.net/") | |||
695 | try: |
|
696 | try: | |
696 | import rpy2.ipython |
|
697 | import rpy2.ipython | |
697 | except ImportError: |
|
698 | except ImportError: | |
698 | pass # Fall back to our own implementation for now |
|
699 | pass # Fall back to our own implementation for now | |
699 | else: |
|
700 | else: | |
700 | return rpy2.ipython.load_ipython_extension(ip) |
|
701 | return rpy2.ipython.load_ipython_extension(ip) | |
701 |
|
702 | |||
702 | ip.register_magics(RMagics) |
|
703 | ip.register_magics(RMagics) | |
703 | # Initialising rpy2 interferes with readline. Since, at this point, we've |
|
704 | # Initialising rpy2 interferes with readline. Since, at this point, we've | |
704 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. |
|
705 | # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. | |
705 | if ip.has_readline: |
|
706 | if ip.has_readline: | |
706 | ip.readline.set_completer_delims(ip.readline_delims) |
|
707 | ip.readline.set_completer_delims(ip.readline_delims) |
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