[BioC] plotpfm has been removed in PWMEnrich?

Robert Stojnic rainmansr at gmail.com
Thu Dec 12 00:28:48 CET 2013 

Dear Fabrice,

This is because your PFM has very little information content. The only 
way to chop off the y axis (which might be misleading to your readers!) 
is to modify the plotting function. If you look at 
PWMEnrich:::seqLogoGrid() you will see these lines of code:

if (ic.scale) {
         ylim <- 2
         ylab <- "Information content"
         facs <- pwm2ic(pwm)
}

You can make a custom copy of this function where you can set your own 
value for ylim. You will also need the pwm2ic() function from the 
seqLogo package. Note that this function takes a probability matrix, 
i.e. "p" from the code below.

Cheers, Robert


On 11/12/13 22:28, Fabrice Tourre wrote:
> Thank you. The plot is not very good. I have attached it.
>
> On Wed, Dec 11, 2013 at 5:22 PM, Robert Stojnic <rainmansr at gmail.com> wrote:
>> Dear Fabrice,
>>
>> pm <- PFMtoPWM(pfm)
>> plot(pm)
>>
>> will plot the logo with correct heights (it will use the calculation I've
>> described below). More advanced options such as changing units (i.e. from
>> bits to e.g. nats) are not supported. If you want to create a custom plot
>> you will have to do it from scratch. Look at the seqLogo package source, or
>> a similar function PWMEnrich:::seqLogoGrid in PWMEnrich.
>>
>> Cheers, Robert
>>
>>
>> On 11/12/13 21:01, Fabrice Tourre wrote:
>>> pm <- PFMtoPWM(pfm)
>>> pm at pwm <- heights
>>> plot(pm)
>>>
>>>
>>> This plot is not good. Because we cannot control y-axis
>>>
>>> On Wed, Dec 11, 2013 at 3:44 PM, Fabrice Tourre <fabrice.ciup at gmail.com>
>>> wrote:
>>>> Dear Robert,
>>>>
>>>> Thank you. When I have the heights matrixs, how can we get a weblogo
>>>> plot?
>>>>
>>>> On Wed, Dec 11, 2013 at 5:44 AM, Robert Stojnic <rainmansr at gmail.com>
>>>> wrote:
>>>>> Hi Fabrice,
>>>>>
>>>>> The negative values are usual as the PWM matrix is defined as log2
>>>>> probability_base / probability_background. So if the any of the
>>>>> probabilities is smaller than 0.25 in your input matrix, this will give
>>>>> a
>>>>> negative value. Maybe you wanted to get the heights of the individual
>>>>> letters in the logo?
>>>>>
>>>>> # convert the count matrix to probabilities
>>>>> p = t(t(pfm) / colSums(pfm))
>>>>>
>>>>> # this is without the small-sample correction, for more information see
>>>>> https://en.wikipedia.org/wiki/Sequence_logo or the original paper
>>>>> h = - colSums(p * log2(p))
>>>>> heights = t(t(p) * (2-h))
>>>>>
>>>>> All the transpositions (calls to t()) are needed to make sure the matrix
>>>>> and
>>>>> vector operations are carried out along the correct dimensions.
>>>>>
>>>>> Cheers, Robert
>>>>>
>>>>>
>>>>> On 10/12/13 16:41, Fabrice Tourre wrote:
>>>>>> PWM always give me some negative value. This strange to me.
>>>>>>
>>>>>> PFMtoPWM(pfm)
>>>>>> An object of class 'PWM'
>>>>>> ID:
>>>>>> Target name:
>>>>>> Frequency matrix:
>>>>>> $pfm
>>>>>>         [,1]    [,2]    [,3]    [,4]    [,5]    [,6]    [,7]    [,8]
>>>>>> [,9]
>>>>>> A 3289112 3286601 3324808 3295086 3297953 3371158 3350851 3380593
>>>>>> 3406893
>>>>>> C 2770671 2771901 2749093 2791942 2791869 2756225 2779305 2780189
>>>>>> 2727296
>>>>>> G 2836085 2853221 2826205 2830413 2845211 2809652 2778112 2742323
>>>>>> 2542202
>>>>>> T 3286234 3270379 3281996 3264661 3247069 3245067 3273834 3278997
>>>>>> 3505711
>>>>>>        [,10]   [,11]   [,12]   [,13]   [,14]   [,15]   [,16]   [,17]
>>>>>> [,18]
>>>>>> A 3293358 2178674 4352405 3227324 3461232 3446487 3259436 3276060
>>>>>> 3271729
>>>>>> C 2663331 2932504 2139363 3052255 2674074 2550187 3005584 2805702
>>>>>> 2844711
>>>>>> G 2467603 2413635 1644787 2028507 2906055 2827872 2948758 3050624
>>>>>> 2971989
>>>>>> T 3757810 4657289 4045547 3874016 3140741 3357556 2968324 3049716
>>>>>> 3093673
>>>>>>        [,19]   [,20]   [,21]
>>>>>> A 3297076 3293868 3334010
>>>>>> C 2853311 2824444 2768038
>>>>>> G 2891960 3017416 2974502
>>>>>> T 3139755 3046374 3105552
>>>>>> Position weight matrix (PWM):
>>>>>> $pwm
>>>>>>            [,1]        [,2]       [,3]       [,4]        [,5]
>>>>>> [,6]
>>>>>> A  0.1110069  0.10990513  0.1265798  0.1136249  0.11487965  0.14655305
>>>>>> C -0.1364558 -0.13581544 -0.1477355 -0.1254222 -0.12545992 -0.14399751
>>>>>> G -0.1027904 -0.09409968 -0.1078251 -0.1056786 -0.09815553 -0.11629972
>>>>>> T  0.1097440  0.10276665  0.1078823  0.1002420  0.09244685  0.09155707
>>>>>>            [,7]       [,8]       [,9]      [,10]      [,11]      [,12]
>>>>>> A  0.1378363  0.1505851  0.1617654  0.1128682 -0.4832408  0.5151216
>>>>>> C -0.1319670 -0.1315082 -0.1592199 -0.1934594 -0.0545581 -0.5095098
>>>>>> G -0.1325864 -0.1512927 -0.2606125 -0.3035809 -0.3354836 -0.8887903
>>>>>> T  0.1042900  0.1065634  0.2030159  0.3032009  0.6127992  0.4096436
>>>>>>             [,13]       [,14]      [,15]       [,16]        [,17]
>>>>>> [,18]
>>>>>> A  0.083647231  0.18459445  0.1784354  0.09793116  0.105270587
>>>>>> 0.10336206
>>>>>> C  0.003184313 -0.18765178 -0.2560881 -0.01904584 -0.118329389
>>>>>> -0.09840908
>>>>>> G -0.586272844 -0.06762917 -0.1069744 -0.04658375  0.002413189
>>>>>> -0.03526240
>>>>>> T  0.347138703  0.04441379  0.1407203 -0.03704261  0.001983716
>>>>>> 0.02262953
>>>>>>            [,19]         [,20]       [,21]
>>>>>> A  0.11449595  0.1130915480  0.13056724
>>>>>> C -0.09405417 -0.1087242780 -0.13782742
>>>>>> G -0.07464358 -0.0133775737 -0.03404303
>>>>>> T  0.04396080  0.0004018867  0.02815854
>>>>>> With background nucleotide frequencies which also serve as
>>>>>> pseudo-count:
>>>>>> $prior.params
>>>>>>       A    C    G    T
>>>>>> 0.25 0.25 0.25 0.25
>>>>>>
>>>>>> On Tue, Dec 10, 2013 at 7:29 AM, Robert Stojnic <rainmansr at gmail.com>
>>>>>> wrote:
>>>>>>> Dear Fabrice,
>>>>>>>
>>>>>>> You can plot the PFM in PWMEnrich by converting it to PWM:
>>>>>>>
>>>>>>> plot(PFMtoPWM(pfm_matrix))
>>>>>>>
>>>>>>> Unfortunately the old function was deprecated. Sorry if it broke your
>>>>>>> code!
>>>>>>>
>>>>>>> Cheers, Robert
>>>>>>>
>>>>>>>
>>>>>>> On 07/12/13 04:41, Fabrice Tourre wrote:
>>>>>>>> Dear expert,
>>>>>>>>
>>>>>>>> I just want to plot PFM using PWMEnrich package. It seems seqlogo
>>>>>>>> cannot do this. But I found in PWMEnrich2.6.2, plotpfm does not
>>>>>>>> exist.
>>>>>>>> How can I plotPFM using new PWMEnrich?
>>>>>>>>
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>>>>>>>>

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