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R'MES	general view	rmes.gaussien	rmes.poisson.composee	rmes.poisson
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Description

Usage

rmes.compar (don1, don2, lg.mot, mod1, mod2, 
             ident=NULL, filtre=NULL, 
             comptage=F,  esperance=F, sigma2=F, 
             conjugue=F,lang="fr")

don1, don2

Character strings equal to the pathnames of the files containing the information to be compared. These files should have been created by one of the following commands: rmes.gaussien, rmes.poisson, rmes.poisson.composee.
If they concern families of words, these must be identical on both files.

Information from don1 will be on the x-axis whereas information from don2 will be on the y-axis. According to don1 and don2:

• A comparison of sequences is done when the files concern the same model (up to the phase), the same count approximation and the same algorithm.
• A comparison of models is done when they concern the same sequence, the same count approximation and eventually the same phase.
• A comparison of phases is done when they concern the same sequence, the same algorithm and the same model.
• A comparison of algorithms, or count approximations, is done when they concern the same sequence and the same model (up to the phase).

Optional Arguments

lg.mot

Length of the words to be represented. It must be less or equal 8. By default, the largest word length found in common in the input files.
Ignored when families of words are compared.

mod1, mod2

Ignored in the current version.

ident

This argument allows to define a list of words or families to be identified on the plot, either by their indices (numbers), or by their names, according to what will be subsequently chosen by the menu (see KIND of DISPLAY).
It introduces a vector that contains words, or family-names, or their indices (words of a given length are numbered according to the lexicographic order a,g,c,t and families to the order on the input files).
(See also the paragraph Note to identify overlapping words or palindromes),

filtre

This argument allows the selection of words or families of words to be displayed. It can be:
- an integer vector of indices of words or families (see the paragraph Note to select overlapping words or palindromes),
- a character vector of words or family-names,
- a character string corresponding to a logical expression: this logical expression must be written with respect to the word counts, the expected counts, the squares of normalizing factors, the statistics or the plotted values associated to the words or families in don1 and don2, via the key-words: val.cmpt.1, val.cmpt.2, val.esp.1, val.esp.2, val.sigma2.1, val.sigma2.2, val.stat.1, val.stat.2, val.plot.1, val.plot.2.
(see example 5 )

comptage, esperance, sigma2

Logical values. Only one can be TRUE that defines what kind of results is presented: the words counts, the expected counts, or the squares of normalizing factors.
By default, the statistics.

conjugue

Logical value. When TRUE, the y-axis coordinate of a word is the quantity related to its conjugate in the file don2.
Ignored when families of words are compared.

lang

When equal to "fr", labels and messages are in french. When equal to "en", labels and messages are in english. By default, they are in french.

Details

The choices are:

0 - QUIT

1 - SELECT A RADIUS CIRCLE
to define a circle of center (0, 0) inside which points are not represented. A null radius deletes the preceding circle.

2 - SELECT A WINDOW
to specify the minimal and maximal bounds of the display window. When one of the bounds is not specified, the current bound is used. The value NA implies the drop-out of a preceding value.

3 - SELECT A KIND OF DISPLAY
to choose how the words are represented. A sub-menu appears with the following choices:

1- POINTS: representation by simple points.
2- NUMBERS: some numbers are put above each point. The correspondance between the numbers and the list of the words appears in the dialog window.
3- NAMES: the word names are put above each point.

NOTE: when some words have been selected (see 6 below) and option NUMBERS or NAMES have been chosen, the numbers or names only appear above the selected points.

4 - CHANGE THE SIZE
to specify a character expansion relative to the device's standard size. For example, 2 implies that characters are twice as big as normal. Reply 1 to reset the normal size.

5 - CHANGE THE SCALE
to specify if the scales on the x-axis and the y-axis should be different when no window bounds are mentionned.

6 - IDENTIFY WORDS (OR FAMILIES)
to modify or reset a list of words (or families of words) to be specifically identified. A sub-menu appears with the following choices:

1 - MODIFICATION: to specify the words to add or to delete to the list, by clicking on the left button of the mouse on the corresponding points (or very near).
The names of the selected words appear beside the corresponding points. Clicking on the middle button of the mouse ends this process.
2 - RESET: to reset the list of selected words to a null-list or to the list introduced by the argument ident.
A null reply implies the go-out from this menu.

7 - SCREEN DISPLAY
to display the plot on the current graphical device unit (X11 by default).

8 - PRINT
to store the plot in a PostScript file. Its name is then asked to the user.

Note

• mot.pal.4,mot.pal.6 and mot.pal.8 contain respectively the word indices corresponding to palindromes of length 4, 6 and 8.
• mot.chev.3, mot.chev.4, ..., until mot.chev.8 contain respectively the word indices corresponding to overlapping words of length 3, 4, 5, 6, 7 and 8.

Examples

> rmes.compar("lambda.gaussien.3_1.0","pt7.gaussien.3_1.0",lg.mot=3,lang="en")

> rmes.compar("coli-codant.gaussien.4_2.1","coli-codant.gaussien.4_2.3",
	       lg.mot=4)

> mot.pal.4 <- c(16,28,40,52,79,91,103,115,142,154,166,178,205,217,229,241)
> rmes.compar("ecomori.gaussien.4_1.0", "ecomori.gaussien.4_2.0", 
	       lg.mot=4, ident=mot.pal.4)
 

> rmes.compar("ecomori.gaussien.4_1.0", "ecomori.gaussien.4_2.0", 
	       lg.mot=4, filtre=mot.pal.4)
 

> rmes.compar("ecomori.gaussien.4_1.0", "ecomori.gaussien.4_2.0", 
	       filtre="val.stat.1>6 & val.stat.2>6")  
 

> rmes.compar("hf-rep.xnxxxxxx_1.0","hf-rep-sans-uptake.xnxxxxxx_1.0",
               ident="gntggtgg",lang="en")
 

Axis Labels