From hp@ge@ @end|ng |rom |redhutch@org  Tue Sep 17 08:52:16 2019
From: hp@ge@ @end|ng |rom |redhutch@org (Pages, Herve)
Date: Tue, 17 Sep 2019 06:52:16 +0000
Subject: [Rd] 
 head.matrix can return 1000s of columns -- limit to n or add
 new argument?
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Message-ID: <f8285123-371f-5d4b-1281-6cc085dba122@fredhutch.org>

Hi,

Alternatively, how about a new glance() generic that would do something 
like this:

 > library(DelayedArray)
 > glance <- DelayedArray:::show_compact_array

 > M <- matrix(rnorm(1e6), nrow = 1000L, ncol = 2000L)
 > glance(M)
<1000 x 2000> matrix object of type "double":
                [,1]        [,2]        [,3] ...    [,1999]    [,2000]
    [1,]  -0.8854896   1.8010288   1.3051341   . -0.4473593  0.4684985
    [2,]  -0.8563415  -0.7102768  -0.9309155   . -1.8743504  0.4300557
    [3,]   1.0558159  -0.5956583   1.2689806   .  2.7292249  0.2608300
    [4,]   0.7547356   0.1465714   0.1798959   . -0.1778017  1.3417423
    [5,]   0.8037360  -2.7081809   0.9766657   . -0.9902788  0.1741957
     ...           .           .           .   .          .          .
  [996,]  0.67220752  0.07804320 -0.38743454   .  0.4438639 -0.8130713
  [997,] -0.67349962 -1.15292067 -0.54505567   .  0.4630923 -1.6287694
  [998,]  0.03374595 -1.68061325 -0.88458368   . -0.2890962  0.2552267
  [999,]  0.47861492  1.25530912  0.19436708   . -0.5193121 -1.1695501
[1000,]  1.52819218  2.23253275 -1.22051720   . -1.0342430 -0.1703396

 > A <- array(rnorm(1e6), c(50, 20, 10, 100))
 > glance(A)
<50 x 20 x 10 x 100> array object of type "double":
,,1,1
             [,1]       [,2]       [,3] ...      [,19]      [,20]
  [1,] 0.78319619 0.82258390 0.09122269   .  1.7288189  0.7968574
  [2,] 2.80687459 0.63709640 0.80844430   . -0.3963161 -1.2768284
   ...          .          .          .   .          .          .
[49,] -1.0696320 -0.1698111  2.0082890   .  0.4488292  0.5215745
[50,] -0.7012526 -2.0818229  0.7750518   .  0.3189076  0.1437394

...

,,10,100
             [,1]       [,2]       [,3] ...      [,19]      [,20]
  [1,]  0.5360649  0.5491561 -0.4098350   .  0.7647435  0.5640699
  [2,]  0.7924093 -0.7395815 -1.3792913   .  0.1980287 -0.2897026
   ...          .          .          .   .          .          .
[49,]  0.6266209  0.3778512  1.4995778   . -0.3820651 -1.4241691
[50,]  1.9218715  3.5475949  0.5963763   .  0.4005210  0.4385623

H.


On 9/16/19 00:54, Michael Chirico wrote:
> Awesome. Gabe, since you already have a workshopped version, would you like
> to proceed? Feel free to ping me to review the patch once it's posted.
> 
> On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler <maechler at stat.math.ethz.ch>
> wrote:
> 
>>>>>>> Michael Chirico
>>>>>>>      on Sun, 15 Sep 2019 20:52:34 +0800 writes:
>>
>>      > Finally read in detail your response Gabe. Looks great,
>>      > and I agree it's quite intuitive, as well as agree against
>>      > non-recycling.
>>
>>      > Once the length(n) == length(dim(x)) behavior is enabled,
>>      > I don't think there's any need/desire to have head() do
>>      > x[1:6,1:6] anymore. head(x, c(6, 6)) is quite clear for
>>      > those familiar with head(x, 6), it would seem to me.
>>
>>      > Mike C
>>
>> Thank you, Gabe, and Michael.
>> I did like Gabe's proposal already back in July but was
>> busy and/or vacationing then ...
>>
>> If you submit this with a patch (that includes changes to both
>> *.R and *.Rd , including some example) as "wishlist" item to R's
>> bugzilla, I'm willing/happy to check and commit this to R-devel.
>>
>> Martin
>>
>>
>>      > On Sat, Jul 13, 2019 at 8:35 AM Gabriel Becker
>>      > <gabembecker at gmail.com> wrote:
>>
>>      >> Hi Michael and Abby,
>>      >>
>>      >> So one thing that could happen that would be backwards
>>      >> compatible (with the exception of something that was an
>>      >> error no longer being an error) is head and tail could
>>      >> take vectors of length (dim(x)) rather than integers of
>>      >> length for n, with the default being n=6 being equivalent
>>      >> to n = c(6, dim(x)[2], <...>, dim(x)[k]), at least for
>>      >> the deprecation cycle, if not permanently. It not
>>      >> recycling would be unexpected based on the behavior of
>>      >> many R functions but would preserve the current behavior
>>      >> while granting more fine-grained control to users that
>>      >> feel they need it.
>>      >>
>>      >> A rapidly thrown-together prototype of such a method for
>>      >> the head of a matrix case is as follows:
>>      >>
>>      >> head2 = function(x, n = 6L, ...) { indvecs =
>>      >> lapply(seq_along(dim(x)), function(i) { if(length(n) >=
>>      >> i) { ni = n[i] } else { ni = dim(x)[i] } if(ni < 0L) ni =
>>      >> max(nrow(x) + ni, 0L) else ni = min(ni, dim(x)[i])
>>      >> seq_len(ni) }) lstargs = c(list(x),indvecs, drop = FALSE)
>>      >> do.call("[", lstargs) }
>>      >>
>>      >>
>>      >> > mat = matrix(1:100, 10, 10)
>>      >>
>>      >> > *head(mat)*
>>      >>
>>      >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
>>      >>
>>      >> [1,] 1 11 21 31 41 51 61 71 81 91
>>      >>
>>      >> [2,] 2 12 22 32 42 52 62 72 82 92
>>      >>
>>      >> [3,] 3 13 23 33 43 53 63 73 83 93
>>      >>
>>      >> [4,] 4 14 24 34 44 54 64 74 84 94
>>      >>
>>      >> [5,] 5 15 25 35 45 55 65 75 85 95
>>      >>
>>      >> [6,] 6 16 26 36 46 56 66 76 86 96
>>      >>
>>      >> > *head2(mat)*
>>      >>
>>      >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
>>      >>
>>      >> [1,] 1 11 21 31 41 51 61 71 81 91
>>      >>
>>      >> [2,] 2 12 22 32 42 52 62 72 82 92
>>      >>
>>      >> [3,] 3 13 23 33 43 53 63 73 83 93
>>      >>
>>      >> [4,] 4 14 24 34 44 54 64 74 84 94
>>      >>
>>      >> [5,] 5 15 25 35 45 55 65 75 85 95
>>      >>
>>      >> [6,] 6 16 26 36 46 56 66 76 86 96
>>      >>
>>      >> > *head2(mat, c(2, 3))*
>>      >>
>>      >> [,1] [,2] [,3]
>>      >>
>>      >> [1,] 1 11 21
>>      >>
>>      >> [2,] 2 12 22
>>      >>
>>      >> > *head2(mat, c(2, -9))*
>>      >>
>>      >> [,1]
>>      >>
>>      >> [1,] 1
>>      >>
>>      >> [2,] 2
>>      >>
>>      >>
>>      >> Now one thing to keep in mind here, is that I think we'd
>>      >> either a) have to make the non-recycling behavior
>>      >> permanent, or b) have head treat data.frames and matrices
>>      >> different with respect to the subsets they grab (which
>>      >> strikes me as a *Bad Plan *(tm)).
>>      >>
>>      >> So I don't think the default behavior would ever be
>>      >> mat[1:6, 1:6], not because of backwards compatibility,
>>      >> but because at least in my intuition that is just not
>>      >> what head on a data.frame should do by default, and I
>>      >> think the behaviors for the basic rectangular datatypes
>>      >> should "stick together". I mean, also because of
>>      >> backwards compatibility, but that could *in theory*
>>      >> change across a long enough deprecation cycle, but the
>>      >> conceptually right thing to do with a data.frame probably
>>      >> won't.
>>      >>
>>      >> All of that said, is head(mat, c(6, 6)) really that much
>>      >> easier to type/better than just mat[1:6, 1:6, drop=FALSE]
>>      >> (I know this will behave differently if any of the dims
>>      >> of mat are less than 6, but if so why are you heading it
>>      >> in the first place ;) )? I don't really have a strong
>>      >> feeling on the answer to that.
>>      >>
>>      >> I'm happy to put a patch for head.matrix,
>>      >> head.data.frame, tail.matrix and tail.data.frame, plus
>>      >> documentation, if people on R-core are interested in
>>      >> this.
>>      >>
>>      >> Note, as most here probably know, and as alluded to
>>      >> above, length(n) > 1 for head or tail currently give an
>>      >> error, so this would be an extension of the existing
>>      >> functionality in the mathematical extension sense, where
>>      >> all existing behavior would remain identical, but the
>>      >> support/valid parameter space would grow.
>>      >>
>>      >> Best, ~G
>>      >>
>>      >>
>>      >> On Fri, Jul 12, 2019 at 4:03 PM Abby Spurdle
>>      >> <spurdle.a at gmail.com> wrote:
>>      >>
>>      >>> > I assume there are lots of backwards-compatibility
>>      >>> issues as well as valid > use cases for this behavior,
>>      >>> so I guess defaulting to M[1:6, 1:6] is out of > the
>>      >>> question.
>>      >>>
>>      >>> Agree.
>>      >>>
>>      >>> > Is there any scope for adding a new argument to
>>      >>> head.matrix that would > allow this flexibility?
>>      >>>
>>      >>> I agree with what you're trying to achieve.  However,
>>      >>> I'm not sure this is as simple as you're suggesting.
>>      >>>
>>      >>> What if the user wants "head" in rows but "tail" in
>>      >>> columns.  Or "head" in rows, and both "head" and "tail"
>>      >>> in columns.  With head and tail alone, there's a
>>      >>> combinatorial explosion.
>>      >>>
>>      >>> Also, when using tail on an unnamed matrix, it may be
>>      >>> desirable to name rows and columns.
>>      >>>
>>      >>> And all of this assumes standard matrix objects.  Add in
>>      >>> a matrix subclasses and related objects, and things get
>>      >>> more complex still.
>>      >>>
>>      >>> As I suggested in a another thread, a few days ago, I'm
>>      >>> planning to write an R package for matrices and
>>      >>> matrix-like objects (possibly extending the Matrix
>>      >>> package), with an initial emphasis on subsetting,
>>      >>> printing and formatting.  So, I'm interested to hear
>>      >>> more suggestions on this topic.
>>      >>>
>>      >>> [[alternative HTML version deleted]]
>>      >>>
>>      >>> ______________________________________________
>>      >>> R-devel at r-project.org mailing list
>>      >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sOZlR-nzy_f_Sje6VGA6IXYQM01BO39OQ2zqA8mtaGI&s=VyNGYbk1jJJqirYBwnhKX60dCp31ArtS62RmXKn86O4&e=
>>      >>>
>>      >>
>>
>>      >   [[alternative HTML version deleted]]
>>
>>      > ______________________________________________
>>      > R-devel at r-project.org mailing list
>>      > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sOZlR-nzy_f_Sje6VGA6IXYQM01BO39OQ2zqA8mtaGI&s=VyNGYbk1jJJqirYBwnhKX60dCp31ArtS62RmXKn86O4&e=
>>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sOZlR-nzy_f_Sje6VGA6IXYQM01BO39OQ2zqA8mtaGI&s=VyNGYbk1jJJqirYBwnhKX60dCp31ArtS62RmXKn86O4&e=
> 

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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[Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?
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