[BioC] plotpfm has been removed in PWMEnrich?

Wed Dec 11 23:28:06 CET 2013

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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>>>>>>> Bioconductor at r-project.org
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>>>>>>>
>
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