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