Module Expr Str Import alias Import alias Import alias Import alias Import alias Import alias Import alias Import alias identifier Import alias identifier Import alias Import alias identifier ImportFrom alias identifier FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults Str AttributeLoad NameLoad attr Str NameLoad NameLoad NameLoad body Expr Str Assign NameStore NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad If CompareEq NameLoad Str body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Num Slice Num Str Assign NameStore Call NameLoad Num NameLoad orelse If CompareEq NameLoad Str body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Num Slice Num Str Assign NameStore Call NameLoad Num NameLoad Assign NameStore Call NameLoad NameLoad Str Assign NameStore ListLoad Assign NameStore ListLoad If CompareIsNot NameLoad NameLoad body Assign NameStore ListLoad If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad orelse Assign NameStore NameLoad If CompareIsNot NameLoad NameLoad body If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr For NameStore NameLoad body Delete SubscriptDel NameLoad Index NameLoad If NameLoad body Assign NameStore Call AttributeLoad SubscriptLoad SubscriptLoad NameLoad Index Num Slice Num attr Str Assign NameStore Call NameLoad Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index NameLoad NameLoad Delete SubscriptDel NameLoad Index Num For NameStore NameLoad body Assign NameStore ListComp Call AttributeLoad NameLoad attr comprehension NameStore Call AttributeLoad SubscriptLoad NameLoad Slice Num attr Str If BoolOpOr UnaryOpNot NameLoad UnaryOpNot ListComp NameLoad comprehension NameStore NameLoad CompareNotEq NameLoad Str body Continue Expr Call AttributeLoad NameLoad attr BinOpAdd Call AttributeLoad NameLoad attr Call NameLoad Lambda arguments args NameParam defaults SubscriptLoad NameLoad Index NameLoad NameLoad Str Str If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr If NameLoad body Assign NameStore Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad Call AttributeLoad Str attr NameLoad orelse Assign NameStore Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return TupleLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults Str ListLoad Str body Expr Str If NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd Str Call AttributeLoad NameLoad attr NameLoad Str Str Assign TupleStore NameStore NameStore AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body If NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd SubscriptLoad NameLoad Index NameLoad Str Expr Call AttributeLoad NameLoad attr BinOpAdd Call AttributeLoad NameLoad attr Call NameLoad Lambda arguments args NameParam defaults BinOpMod NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad Str Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Num Num decorator_list FunctionDef arguments args NameParam defaults NameLoad body If CompareIs NameLoad NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword TupleLoad Str Str Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword TupleLoad Str Str Str Str Str Str Str Str Str Str Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword TupleLoad Str Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword Str keyword NameLoad keyword Str keyword NameLoad keyword ListLoad keyword ListLoad keyword Num keyword Str keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword Str keyword NameLoad keyword Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If BoolOpAnd CompareEq Call NameLoad NameLoad Num UnaryOpNot AttributeLoad NameLoad attr body Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index Num If CompareNotIn AttributeLoad NameLoad attr TupleLoad Str Str body Assign AttributeStore NameLoad attr Call NameLoad Lambda arguments args NameParam defaults BinOpSub Call NameLoad NameLoad Num Call AttributeLoad AttributeLoad NameLoad attr attr Str If AttributeLoad NameLoad attr body AugAssignSub AttributeStore NameLoad attr Num If AttributeLoad NameLoad attr body AugAssignSub AttributeStore NameLoad attr Num Assign NameStore Dict Assign NameStore ListLoad If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr Str attr orelse Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call NameLoad Lambda arguments args NameParam defaults CompareNotEq SubscriptLoad NameLoad Index Num Str NameLoad If CompareEq Call NameLoad NameLoad Num body If AttributeLoad NameLoad attr body Raise Call NameLoad Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr Return Assign TupleStore NameStore NameStore NameStore NameStore Call NameLoad NameLoad Str keyword AttributeLoad NameLoad attr keyword NameLoad keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore NameStore NameStore Call NameLoad NameLoad Str keyword AttributeLoad NameLoad attr keyword NameLoad keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str NameLoad Assign NameStore SubscriptLoad Call NameLoad Str Index Num If CompareGtE AttributeLoad NameLoad attr Num body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad Call NameLoad NameLoad NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr Str NameLoad For NameStore AttributeLoad NameLoad attr body If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str Expr Call NameLoad AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str orelse If CompareEq NameLoad Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd Call AttributeLoad Str attr TupleLoad Str Str Str Str Str Str Str Str Str For NameStore Call NameLoad BinOpSub Call NameLoad NameLoad Num body For NameStore Call NameLoad BinOpAdd NameLoad Num Call NameLoad NameLoad body TryExcept body Assign NameStore Call NameLoad BinOpMod Str TupleLoad BinOpAdd NameLoad Num BinOpAdd NameLoad Num handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad Str Str Str Num Str Str orelse Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Str Index Num Call AttributeLoad NameLoad attr Call NameLoad SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num SubscriptLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr Str Index Num SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num orelse If CompareEq NameLoad Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd Call AttributeLoad Str attr TupleLoad Str Str Str Str Str Str Str Str For NameStore Call NameLoad BinOpSub Call NameLoad NameLoad Num body For NameStore Call NameLoad BinOpAdd NameLoad Num Call NameLoad NameLoad body Assign NameStore Call NameLoad BinOpMod Str TupleLoad BinOpAdd NameLoad Num BinOpAdd NameLoad Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Call AttributeLoad NameLoad attr Call NameLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str SubscriptLoad SubscriptLoad NameLoad Index Str Index Str SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str orelse If CompareEq NameLoad Str body Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Str keyword AttributeLoad NameLoad attr keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call NameLoad AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str If AttributeLoad NameLoad attr body If CompareIn Str AttributeLoad NameLoad attr body Assign NameStore Call NameLoad Str Assign NameStore ListComp NameLoad comprehension NameStore Call NameLoad Call NameLoad NameLoad CompareNotEq SubscriptLoad NameLoad Index NameLoad NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr BinOpMod Str Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword ListComp BinOpAdd NameLoad Num comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad If NameLoad body Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad If AttributeLoad NameLoad attr body Assign NameStore BinOpMod Str AttributeLoad NameLoad attr orelse Assign NameStore Str If BoolOpAnd CompareIsNot AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad body AugAssignAdd NameStore BinOpMod Str Call AttributeLoad Str attr NameLoad If AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str AugAssignAdd NameStore BinOpMod Str TupleLoad NameLoad NameLoad orelse Assign TupleStore NameStore NameStore TupleLoad Str Str If AttributeLoad NameLoad attr body AugAssignAdd NameStore Str If AttributeLoad NameLoad attr body AugAssignAdd NameStore BinOpMod Str AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body AugAssignAdd NameStore BinOpMod Str Call NameLoad Call NameLoad NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str If AttributeLoad NameLoad attr body AugAssignAdd NameStore BinOpMod Str Call NameLoad Call NameLoad NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str If AttributeLoad NameLoad attr body If Call AttributeLoad AttributeLoad NameLoad attr attr Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If Call AttributeLoad AttributeLoad NameLoad attr attr Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword Num keyword Num keyword Str orelse If Call AttributeLoad AttributeLoad NameLoad attr attr Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword Num keyword Num keyword Str For NameStore AttributeLoad NameLoad attr body If CompareLt NameLoad Num body Assign NameStore Str Assign NameStore Str orelse If CompareLt NameLoad Num body Assign NameStore Str Assign NameStore Str orelse Assign NameStore Str Assign NameStore Str If CompareEq NameLoad Str body Expr Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad If CompareEq NameLoad Str body Expr Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad Assign NameStore Call NameLoad Str Expr Call NameLoad Str Assign NameStore Call NameLoad Str Expr Call NameLoad Str Expr Call NameLoad Str Expr Call NameLoad Str Expr Call NameLoad Str Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Call NameLoad Str NameLoad Num keyword Num orelse If CompareEq NameLoad Str body If AttributeLoad NameLoad attr body Expr Call NameLoad Str orelse Expr Call NameLoad Str If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad keyword AttributeLoad NameLoad attr keyword Str keyword NameLoad keyword Num orelse Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str keyword AttributeLoad NameLoad attr keyword NameLoad keyword Num orelse If CompareEq NameLoad Str body AugAssignAdd NameStore BinOpMod Str AttributeLoad NameLoad attr If CompareGt Call NameLoad ListComp Call NameLoad NameLoad comprehension NameStore NameLoad BinOpDiv Num Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str Str NameLoad AugAssignAdd NameStore Str Expr Call NameLoad Str Expr Call NameLoad BinOpMod Str NameLoad orelse If BoolOpOr CompareEq NameLoad Str CompareEq NameLoad Str body If UnaryOpNot AttributeLoad NameLoad attr body AugAssignAdd NameStore Str If CompareGt Call NameLoad ListComp Call NameLoad NameLoad comprehension NameStore NameLoad BinOpDiv Num Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str Str NameLoad AugAssignAdd NameStore Str Expr Call NameLoad Str Expr Call NameLoad BinOpMod Str NameLoad orelse If CompareEq NameLoad Str body If UnaryOpNot AttributeLoad NameLoad attr body AugAssignAdd NameStore BinOpMod Str NameLoad If CompareGt Call NameLoad ListComp Call NameLoad NameLoad comprehension NameStore NameLoad BinOpDiv Num Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str Str NameLoad AugAssignAdd NameStore Str Expr Call NameLoad Str Expr Call NameLoad BinOpMod Str NameLoad orelse If CompareEq NameLoad Str body If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr keyword Call AttributeLoad NameLoad attr Num Num Num Num Expr Call NameLoad Str Expr Call NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Num keyword NameLoad keyword Num keyword Num orelse If CompareIn NameLoad TupleLoad Str Str Str body If CompareEq NameLoad Str body Assign NameStore ListLoad For NameStore Call NameLoad BinOpSub Call NameLoad NameLoad Num body For NameStore Call NameLoad BinOpAdd NameLoad Num Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad orelse If CompareEq NameLoad Str body Assign NameStore ListLoad For NameStore Call NameLoad Num Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr TupleLoad Num NameLoad orelse If CompareEq NameLoad Str body Assign NameStore ListLoad For NameStore Call NameLoad BinOpSub Call NameLoad NameLoad Num body For NameStore Call NameLoad BinOpAdd NameLoad Num Call NameLoad NameLoad body If CompareEq SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad body Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Break Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr BinOpDiv Call NameLoad Call NameLoad NameLoad NameLoad Assign NameStore Num Assign NameStore Num Assign TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call NameLoad BinOpMod Str TupleLoad BinOpMult NameLoad NameLoad NameLoad NameLoad For TupleStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad Lambda arguments args NameParam defaults BoolOpAnd CompareNotIn SubscriptLoad NameLoad Index Num TupleLoad Call NameLoad Str NameLoad NameLoad CompareNotIn SubscriptLoad NameLoad Index Num TupleLoad Call NameLoad Str NameLoad NameLoad Call NameLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Index Num SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Index Num TryExcept body Expr Call NameLoad BinOpMod Str TupleLoad BinOpAdd NameLoad Num BinOpAdd NameLoad Num SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Print BinOpMod Str TupleLoad SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad If AttributeLoad NameLoad attr body Expr Call SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr Str If UnaryOpNot AttributeLoad NameLoad attr body If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr Call NameLoad Expr Call AttributeLoad NameLoad attr orelse Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
r_table2scatter.py - R based plots and stats
============================================

:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python

Purpose
-------

This script reads a table from a file or stdin. 
It can compute various stats (correlations, ...)
and/or plot the data using R.

Usage
-----

Example::

   python r_table2scatter.py --help

Type::

   python r_table2scatter.py --help

for command line help.

Command line options
--------------------

 N/A os N/A sys N/A string N/A re N/A tempfile N/A math N/A code N/A CGAT.Experiment E N/A CGAT.MatlabTools MatlabTools N/A numpy N/A CGAT.Stats Stats rpy2.robjects r R readTable N/A N/A lines assign separator numeric_type take_columns headers row_names colours N/A N/A numpy float all True None None N/A N/A read a matrix. There probably is a routine for this in Numpy, which
    I haven't found yet.

    The advantage of using rpy's mechanism is to allow for 
    missing values.

    row_names: column with row names
     N/A take take_columns N/A N/A handle name N/A N/A tempfile mkstemp N/A N/A N/A os close handle N/A N/A take_columns all N/A N/A num_cols N/A len N/A N/A string split N/A N/A lines N/A 0 N/A -1 N/A take N/A range 0 num_cols N/A N/A N/A take_columns all-but-first N/A N/A num_cols N/A len N/A N/A string split N/A N/A lines N/A 0 N/A -1 N/A take N/A range 1 num_cols N/A outfile N/A open name w N/A c N/A N/A to_delete N/A N/A N/A row_names None N/A N/A legend N/A N/A N/A take_columns all N/A N/A N/A N/A to_delete append row_names N/A N/A legend None N/A N/A colours None N/A N/A N/A take_columns all N/A N/A N/A N/A to_delete append colours N/A N/A N/A to_delete sort N/A N/A N/A to_delete reverse N/A x to_delete N/A N/A N/A take N/A x N/A headers N/A N/A headers N/A N/A N/A N/A lines N/A 0 N/A -1 split N/A headers N/A map N/A N/A N/A x N/A N/A headers N/A x take N/A N/A lines N/A 0 N/A l lines N/A N/A data N/A N/A N/A x strip N/A x N/A N/A N/A l N/A -1 split N/A N/A N/A data N/A N/A x N/A x data N/A x N/A N/A N/A N/A N/A outfile write N/A N/A N/A string join N/A map N/A N/A N/A x N/A N/A data N/A x take N/A N/A row_names None N/A N/A N/A N/A legend append N/A data N/A row_names N/A N/A colours None N/A N/A N/A N/A c append N/A data N/A colours N/A N/A N/A outfile close N/A headers N/A N/A matrix N/A R N/A %s <- read.table( '%s', na.string = c("NA", "na", 'nan', 'NaN'), col.names=c('%s'), sep="	" ) N/A assign name N/A N/A ',' join headers N/A N/A matrix N/A R N/A %s <- read.table( '%s', na.string = c("NA", "na", 'nan', 'NaN'), col.names=headers, sep="	" ) N/A assign name N/A N/A N/A os remove name N/A N/A matrix headers c legend N/A writeMatrix N/A N/A file matrix separator headers format N/A N/A %f N/A N/A write a matrix to file.

    if headers are given, add them to columns and rows.
     N/A headers N/A N/A N/A N/A file write N/A N/A N/A N/A string join headers N/A N/A nrows ncols N/A matrix shape N/A x N/A range nrows N/A N/A headers N/A N/A N/A N/A file write N/A N/A headers N/A x N/A N/A N/A file write N/A N/A N/A string join N/A map N/A N/A N/A x N/A N/A format x N/A matrix N/A x N/A FuncScatterDiagonal N/A N/A data N/A N/A N/A N/A N/A R points data N/A N/A N/A R abline 0 1 N/A main N/A N/A argv N/A None N/A N/A N/A argv None N/A N/A argv N/A sys argv N/A parser N/A N/A E OptionParser version %prog version: $Id: r_table2scatter.py 2782 2009-09-10 11:40:29Z andreas $ N/A N/A N/A parser add_option -c --columns dest columns type string help columns to take from table. Choices are 'all', 'all-but-first' or a ','-separated list of columns. N/A N/A N/A parser add_option --logscale dest logscale type string help log-transform one or both axes [default=%Default]. N/A N/A N/A parser add_option -a --hardcopy dest hardcopy type string help write hardcopy to file [default=%default]. metavar FILE N/A N/A N/A parser add_option -f --file dest input_filename type string help filename with table data [default=%default]. metavar FILE N/A N/A N/A parser add_option -2 --file2 dest input_filename2 type string help additional data file [default=%default]. metavar FILE N/A N/A N/A parser add_option -s --stats dest statistics type choice choices N/A correlation spearman pearson count help statistical quantities to compute [default=%default] action append N/A N/A N/A parser add_option -p --plot dest plot type choice choices N/A scatter pairs panel bar bar-stacked bar-besides 1_vs_x matched boxplot scatter+marginal scatter-regression help plots to plot [default=%default] action append N/A N/A N/A parser add_option -t --threshold dest threshold type float help min threshold to use for counting method [default=%default]. N/A N/A N/A parser add_option -o --colours dest colours type int help column with colour information [default=%default]. N/A N/A N/A parser add_option -l --plot-labels dest labels type string help column labels for x and y in matched plots [default=%default]. N/A N/A N/A parser add_option -d --add-diagonal dest add_diagonal action store_true help add diagonal to plot [default=%default]. N/A N/A N/A parser add_option -e --plot-legend dest legend type int help column with legend [default=%default]. N/A N/A N/A parser add_option -r --options dest r_options type string help R plotting options [default=%default]. N/A N/A N/A parser add_option --format dest format type choice choices N/A full sparse help output format [default=%default]. N/A N/A N/A parser add_option --title dest title type string help plot title [default=%default]. N/A N/A N/A parser add_option --xrange dest xrange type string help x viewing range of plot [default=%default]. N/A N/A N/A parser add_option --yrange dest yrange type string help y viewing range of plot[default=%default]. N/A N/A N/A parser add_option --allow-empty-file dest fail_on_empty action store_false help do not fail on empty input [default=%default]. N/A N/A N/A parser add_option --fail-on-empty dest fail_on_empty action store_true help fail on empty input [default=%default]. N/A N/A N/A parser set_defaults hardcopy None input_filename input_filename2 None columns all logscale None statistics N/A plot N/A threshold 0.0 labels x,y colours None diagonal False legend None title None xrange None yrange None r_options fail_on_empty True format full N/A N/A options args N/A N/A E Start parser N/A N/A N/A N/A len args 1 N/A N/A options input_filename N/A N/A N/A options input_filename N/A args N/A 0 N/A N/A N/A options columns N/A all all-but-first N/A N/A N/A options columns N/A map N/A N/A N/A x N/A N/A N/A int x 1 N/A N/A N/A options columns split , N/A N/A options colours N/A N/A N/A options colours 1 N/A N/A options legend N/A N/A N/A options legend 1 N/A table N/A N/A headers N/A N/A N/A options input_filename N/A N/A lines N/A N/A N/A open N/A options input_filename r readlines N/A N/A lines N/A N/A N/A sys stdin readlines N/A lines N/A filter N/A N/A N/A x N/A N/A N/A x N/A 0 # lines N/A N/A N/A len lines 0 N/A N/A N/A options fail_on_empty N/A N/A N/A IOError no input N/A N/A N/A E warn empty input N/A N/A N/A E Stop N/A N/A N/A matrix headers colours legend N/A readTable lines matrix take_columns N/A options columns headers True colours N/A options colours row_names N/A options legend N/A N/A options input_filename2 N/A N/A N/A matrix2 headers2 colours2 legend2 N/A readTable lines matrix2 take_columns N/A options columns headers True colours N/A options colours row_names N/A options legend N/A N/A N/A R assign headers headers N/A ndata N/A N/A R length( matrix[,1] ) N/A 0 N/A N/A N/A options loglevel 1 N/A N/A N/A N/A N/A options stdlog write N/A # read matrix: %ix%i
 N/A N/A len headers ndata N/A colours N/A N/A N/A N/A R assign colours colours N/A method N/A options statistics N/A N/A N/A method correlation N/A N/A cor N/A N/A R cor matrix use pairwise.complete.obs N/A N/A writeMatrix N/A sys stdout cor headers headers format %5.2f N/A N/A N/A method pearson N/A N/A N/A N/A N/A options stdout write N/A N/A N/A join N/A var1 var2 coeff passed pvalue n method alternative N/A x N/A range N/A N/A len headers 1 N/A N/A y N/A range N/A x 1 N/A len headers N/A N/A N/A N/A result N/A R N/A cor.test( matrix[,%i], matrix[,%i] ) N/A N/A x 1 N/A y 1 N/A N/A N/A N/A rpy RPyException N/A msg N/A N/A N/A N/A E warn N/A correlation not computed for columns %i(%s) and %i(%s): %s N/A x N/A headers N/A x y N/A headers N/A y msg N/A N/A N/A N/A options stdout write N/A %s	%s	%s	%s	%s	%i	%s	%s
 N/A N/A headers N/A x N/A headers N/A y na na na 0 na na N/A N/A N/A N/A N/A options stdout write N/A %s	%s	%6.4f	%s	%e	%i	%s	%s
 N/A N/A headers N/A x N/A headers N/A y N/A N/A N/A N/A N/A result rx2 estimate rx2 cor N/A 0 N/A N/A Stats getSignificance N/A float N/A N/A N/A result rx2 p.value N/A 0 N/A N/A N/A result rx2 p.value N/A 0 N/A N/A N/A N/A N/A result rx2 parameter rx2 df N/A 0 N/A N/A N/A result rx2 method N/A 0 N/A N/A N/A result rx2 alternative N/A 0 N/A N/A N/A method spearman N/A N/A N/A N/A N/A options stdout write N/A N/A N/A join N/A var1 var2 coeff passed pvalue method alternative N/A x N/A range N/A N/A len headers 1 N/A N/A y N/A range N/A x 1 N/A len headers N/A N/A result N/A R N/A cor.test( matrix[,%i], matrix[,%i], method='spearman') N/A N/A x 1 N/A y 1 N/A N/A N/A N/A options stdout write N/A %s	%s	%6.4f	%s	%e	%i	%s	%s
 N/A N/A headers N/A x N/A headers N/A y N/A N/A result N/A estimate N/A rho N/A N/A Stats getSignificance N/A float N/A result N/A p.value N/A result N/A p.value N/A N/A result N/A parameter N/A df N/A result N/A method N/A result N/A alternative N/A N/A N/A method count N/A N/A N/A m r c N/A N/A MatlabTools ReadMatrix N/A open N/A options input_filename r take N/A options columns headers True N/A mask N/A N/A numpy greater m N/A options threshold N/A counts N/A N/A numpy dot N/A N/A numpy transpose mask mask N/A N/A writeMatrix N/A options stdout counts headers c format %i N/A N/A options plot N/A N/A N/A pairs N/A options plot N/A N/A colsums N/A R colSums( is.na(matrix )) N/A take N/A x N/A x N/A range N/A len colsums N/A N/A colsums N/A x ndata N/A take N/A N/A N/A N/A E warn N/A removing empty columns %s before plotting N/A str take N/A matrix N/A N/A R subset matrix select N/A N/A x 1 N/A x take N/A N/A N/A R assign matrix matrix N/A headers N/A N/A headers N/A x N/A x take N/A legend N/A N/A legend N/A N/A headers N/A x N/A x take N/A N/A options r_options N/A N/A extra_options N/A , %s N/A options r_options N/A N/A extra_options N/A N/A N/A N/A options legend None N/A len legend N/A N/A extra_options N/A , legend=c('%s') N/A N/A ',' join legend N/A N/A options labels N/A N/A N/A xlabel ylabel N/A N/A N/A options labels split , N/A extra_options N/A , xlab='%s', ylab='%s' N/A xlabel ylabel N/A N/A N/A xlabel ylabel N/A N/A N/A options colours N/A N/A extra_options , col=colours N/A N/A options logscale N/A N/A extra_options N/A , log='%s' N/A options logscale N/A N/A options xrange N/A N/A extra_options N/A , xlim=c(%f,%f) N/A tuple N/A map float N/A N/A N/A options xrange split , N/A N/A options yrange N/A N/A extra_options N/A , ylim=c(%f,%f) N/A tuple N/A map float N/A N/A N/A options yrange split , N/A N/A options hardcopy N/A N/A N/A N/A N/A options hardcopy endswith .eps N/A N/A N/A N/A R postscript N/A options hardcopy N/A N/A N/A N/A N/A options hardcopy endswith .png N/A N/A N/A N/A R png N/A options hardcopy width 1024 height 768 type cairo N/A N/A N/A N/A N/A options hardcopy endswith .jpg N/A N/A N/A N/A R jpg N/A options hardcopy width 1024 height 768 type cairo N/A method N/A options plot N/A N/A N/A ndata 100 N/A N/A point_size 1 N/A pch o N/A N/A N/A ndata 1000 N/A N/A point_size 1 N/A pch o N/A N/A point_size 0.5 N/A pch . N/A N/A method scatter N/A N/A N/A R N/A plot( matrix[,1], matrix[,2], cex=%s, pch="o" %s) N/A point_size extra_options N/A N/A method scatter-regression N/A N/A N/A R N/A plot( matrix[,1], matrix[,2], cex=%s, pch="o" %s) N/A point_size extra_options N/A dat N/A R dat <- data.frame(x = matrix[,1], y = matrix[,2]) N/A N/A R new <- data.frame(x = seq( min(matrix[,1]), max(matrix[,1]), (max(matrix[,1]) - min(matrix[,1])) / 100)) N/A mod N/A R mod <- lm( y ~ x, dat) N/A N/A R predict(mod, new, se.fit = TRUE) N/A N/A R pred.w.plim <- predict(mod, new, interval="prediction") N/A N/A R pred.w.clim <- predict(mod, new, interval="confidence") N/A N/A R matpoints(new$x,cbind(pred.w.clim, pred.w.plim[,-1]), lty=c(1,2,2,3,3), type="l") N/A N/A N/A R mtext N/A y = %f * x + %f, r=%6.4f, n=%i N/A N/A N/A mod N/A coefficients N/A x N/A N/A mod N/A coefficients N/A (Intercept) N/A R cor( dat )[2] ndata 3 cex 1.0 N/A N/A N/A method pairs N/A N/A N/A options add_diagonal N/A N/A N/A R panel.hist <- function( x,y,...  ) { points(x,y,...); abline(0,1); } N/A N/A N/A R panel.hist <- function( x,y,...  ) { points(x,y,...); } N/A N/A options colours N/A N/A N/A N/A R pairs matrix pch pch col colours main N/A options title panel panel.hist labels headers cex_labels 2.0 N/A N/A N/A N/A R pairs matrix pch pch panel panel.hist main N/A options title labels headers cex_labels 2.0 N/A N/A N/A method boxplot N/A N/A extra_options N/A ,main='%s' N/A options title N/A N/A N/A max N/A N/A len x N/A x headers N/A 40 N/A len headers N/A N/A extra_options N/A N/A re sub , xlab='[^']+' extra_options N/A extra_options , names.arg=headers, las=2 N/A N/A R op <- par(mar=c(11,4,4,2)) N/A N/A R N/A boxplot( matrix %s) extra_options N/A N/A N/A N/A method bar N/A method bar-stacked N/A N/A N/A N/A options colours N/A N/A extra_options , col=rainbow(5) N/A N/A N/A max N/A N/A len x N/A x headers N/A 40 N/A len headers N/A N/A extra_options N/A N/A re sub , xlab='[^']+' extra_options N/A extra_options , names.arg=headers, las=2 N/A N/A R op <- par(mar=c(11,4,4,2)) N/A N/A R N/A barplot(as.matrix(matrix), %s) extra_options N/A N/A N/A method bar-besides N/A N/A N/A N/A options colours N/A N/A extra_options N/A , col=rainbow(%i) ndata N/A N/A N/A max N/A N/A len x N/A x headers N/A 40 N/A len headers N/A N/A extra_options N/A N/A re sub , xlab='[^']+' extra_options N/A extra_options , names.arg=headers, las=2 N/A N/A R op <- par(mar=c(11,4,4,2)) N/A N/A R N/A barplot(as.matrix(matrix), beside=TRUE %s) extra_options N/A N/A N/A method scatter+marginal N/A N/A N/A options title N/A N/A N/A N/A R par oma N/A N/A R c 0 0 4 0 N/A N/A R matrix N/A N/A R N/A 
x <- matrix[,1];
y <- matrix[,2];
xhist <- hist(x, breaks=20, plot=FALSE);
yhist <- hist(y, breaks=20, plot=FALSE);
top <- max(c(xhist$counts, yhist$counts));
nf <- layout(matrix(c(2,0,1,3),2,2,byrow=TRUE), c(3,1), c(1,3), respect=TRUE );
par(mar=c(3,3,1,1)) ;
plot(x, y, cex=%s, pch="o" %s) ;
par(mar=c(0,3,1,1)) ;
barplot(xhist$counts, axes=FALSE, ylim=c(0, top), space=0 ) ;
par(mar=c(3,0,1,1)) ;
title(main='%s');
barplot(yhist$counts, axes=FALSE, xlim=c(0, top), space=0, horiz=TRUE ) ;
title(main='%s');
 N/A point_size extra_options xlabel ylabel N/A N/A options title N/A N/A N/A N/A R mtext N/A options title 3 outer True line 1 cex 1.5 N/A N/A N/A method N/A panel 1_vs_x matched N/A N/A N/A method panel N/A N/A pairs N/A N/A x N/A range N/A N/A len headers 1 N/A N/A y N/A range N/A x 1 N/A len headers N/A N/A N/A N/A pairs append N/A x y N/A N/A N/A method 1_vs_x N/A N/A pairs N/A N/A x N/A range 1 N/A len headers N/A N/A N/A N/A pairs append N/A 0 x N/A N/A N/A method matched N/A N/A pairs N/A N/A x N/A range N/A N/A len headers 1 N/A N/A y N/A range N/A x 1 N/A len headers N/A N/A N/A N/A headers N/A x N/A headers N/A y N/A N/A N/A N/A pairs append N/A x y N/A N/A w N/A int N/A N/A math ceil N/A N/A math sqrt N/A len pairs N/A h N/A int N/A N/A math ceil N/A N/A float N/A len pairs w N/A PosInf inf N/A NegInf -inf N/A N/A xlabel ylabel N/A N/A N/A options labels split , N/A N/A R N/A layout(matrix(seq(1,%i), %i, %i, byrow = TRUE)) N/A N/A w h w h N/A N/A a b pairs N/A N/A new_matrix N/A filter N/A N/A N/A x N/A N/A N/A N/A x N/A 0 N/A N/A float nan PosInf NegInf N/A N/A x N/A 1 N/A N/A float nan PosInf NegInf N/A zip N/A N/A N/A N/A matrix N/A a values N/A 0 N/A N/A N/A N/A matrix N/A b values N/A 0 N/A N/A N/A N/A R N/A plot(matrix[,%i], matrix[,%i], main='%s versus %s', cex=0.5, pch=".", xlab='%s', ylab='%s' ) N/A N/A a 1 N/A b 1 N/A headers N/A b N/A headers N/A a xlabel ylabel N/A N/A N/A N/A rpy RException N/A msg N/A N/A N/A could not plot %s versus %s: %s N/A N/A headers N/A b N/A headers N/A a msg N/A N/A options hardcopy N/A N/A N/A N/A R N/A dev.off N/A N/A N/A E info matrix added as >matrix< in R. N/A N/A N/A options hardcopy N/A N/A N/A options input_filename N/A N/A interpreter N/A N/A code InteractiveConsole N/A globals N/A N/A N/A interpreter interact N/A N/A N/A N/A E info can not start new interactive session as input has come from stdin. N/A N/A N/A E Stop N/A N/A N/A __name__ __main__ N/A N/A N/A main