Error from Histogram in local galaxy installation : 'x' must be numeric - galaxy-user

11 Mar 2010


      Using an upload of  test-data/2.tabular  as  test dataset
My local installations  (Mac and Linux)  of galaxy reports this error 
for   Histogram:
An error occurred running this job: Error in hist.default(list(68, 71, 
62, 75, 58, 60, 67, 68, 71, 69), xlab = "V1", :
'x' must be numeric
This works without error at:   http://main.g2.bx.psu.edu/
I looked at the code in   tools/plotting/histogram.py    and it doesn't 
make sense to me.
Why does it create matrix = []  which it seems to use as a 2-Dim array? 
R hist()   seems to only take an R Vector.
Are there any version changes to R, Rpy, or NumPy that might have 
changed how this operates?
I executed some of that code interactively and got  the same error message:
$ python
Python 2.6.4 (r264:75706, Mar  9 2010, 10:00:44)
[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
...
...
...
import sys
from rpy import *
matrix = []
vals = ["23","14","32","25","12","9","35","18","24"]
for i in vals:
...     row = [];row.append(float(i));matrix.append(row)
...
...
...
...
matrix
[[23.0], [14.0], [32.0], [25.0], [12.0], [9.0], [35.0], [18.0], [24.0]]
...
...
...
a = array(matrix)
r.pdf("histtest.pdf", 8, 8)
title = "Histogram Test";xlab="Count";breaks="Sturges"
r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks )
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
rpy.RPy_RException: Error in hist.default(list(23, 14, 32, 25, 12, 9, 
35, 18, 24), xlab = "Count",  :
 'x' must be numeric
...
...
...
a array([[ 23.],
[ 14.],
      [ 32.],
      [ 25.],
      [ 12.],
      [  9.],
      [ 35.],
      [ 18.],
      [ 24.]])
...
...
...
# Now JJ tries creating just a vector instead of using matrix
...
...
...
...
v = []
for i in vals:
...     v.append(float(i))
...
...
...
...
v
[23.0, 14.0, 32.0, 25.0, 12.0, 9.0, 35.0, 18.0, 24.0]
...
...
...
r.hist(v, probability=True, main=title, xlab=xlab, breaks=breaks )
{'density': [0.022222217777778667, 0.044444444444444446, 
0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 
'equidist': True, 'breaks': [5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0], 
'intensities': [0.022222217777778667, 0.044444444444444446, 
0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 
'counts': [1, 2, 1, 3, 0, 2], 'xname': 'c(23, 14, 32, 25, 12, 9, 35, 18, 
24)', 'mids': [7.5, 12.5, 17.5, 22.5, 27.5, 32.5]}
...
...
...
a = array(v)
r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks )
{'density': [0.022222217777778667, 0.044444444444444446, 
0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 
'equidist': True, 'breaks': [5.0, 10.0, 15.0, 20.0, 25.0, 30.0, 35.0], 
'intensities': [0.022222217777778667, 0.044444444444444446, 
0.02222222222222223, 0.066666666666666666, 0.0, 0.044444444444444446], 
'counts': [1, 2, 1, 3, 0, 2], 'xname': 'c(23, 14, 32, 25, 12, 9, 35, 18, 
24)', 'mids': [7.5, 12.5, 17.5, 22.5, 27.5, 32.5]}
...
...
...
r.dev_off()
{'null device': 1}
...
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