[BioC] plotpfm has been removed in PWMEnrich?

[Fabrice Tourre]

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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>