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