Question: Regarding somatic signature package
0
3.3 years ago by
sj110
sj110 wrote:

Hi Sir,

The previous problem is solved,thanks for your effort.I have a question the plot that is generated for Mutation spectrum using this function -

plotMutationSpectrum(sca_motifs, "study") gives Contribution vs Motif plot.What does Contribution means here?

Another Question regarding Mutation signature plot is that while generating the plot multiple times(generated 5 times),we are getting different results(results are not similar in all 5 plots) using this function-

plotSignatures(sigs_nmf) + ggtitle("Somatic Signatures: NMF - Barchart")


Why this is occurring,not able to find out.Need your help.Looking for your response.

Thanks

Swati.

somaticsignatures • 589 views
modified 3.3 years ago by Julian Gehring1.3k • written 3.3 years ago by sj110

Could you please provide a small reproducible example for the second question?

I have to send plots but I am not getting any attachment option here.Plz help.Also I need the answer of first question, what does contribution means for this plot fuction

plotMutationSpectrum(sca_motifs, "study") as it gives Contribution vs Motif plot.

See the FAQ for one way to include images. For a reproducible example, Julian is looking for a small piece of code that he can run on his computer (so obviously it can't be with your data, maybe with data used in the examples in the SomaticSignatures package). The FAQ also has a section on writing reproducible examples.

If we could answer an older question of you, you can mark an answer as accepted and/or upvote it. This way, other users which similar questions can benefit better from the questions and answers.

0
3.3 years ago by
sj110
sj110 wrote:

Hi Sir,

Please have a look at this link https://www.dropbox.com/s/p30pdl0a7ifdv7a/ss1_ss2.png?dl=0 where I have attached an image of two plots which are slightly different to each other. I have used this function

plotSignatures(sigs_nmf) + ggtitle("Somatic Signatures: NMF - Barchart") and run this 10 times on the dataset supplied with the package,the plot on the right side occurred 8 times whereas the plot on the left side occurred 2 times.

We have also run this for our dataset but the dissimilarity is more.We don't know the reason.So, please help us.

Another one is the plotMutationSpectrum(sca_motifs, "study") function,have a look at this link https://www.dropbox.com/s/zkcux54pe0uu2re/Mutation_spectrum.png?dl=0

it results into Contribution vs Motif plot.What does Contribution means here??

Thanks

Swati

0
3.3 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

plotMutationSpectrum visualises the observed mutational spectrum 'M', and contribution indicates the how often a certain motif is present in the variant calls for each sample/group. Depending on the arguments of the function, this is either represented as counts or frequencies - you can have a look at the vignette, the documentation of the function as well as the publications of the methods that discuss all this in detail.

Regarding your other question, can you please provide all relevant code that you have been using for producing these figures, in the form of a minimal, reproducible example? In particular, please indicate which parts of the code have been run only once and which ones multiple times. As Martin outlined, this is essential for me or others here to understand in detail what you have been doing.

Hi Sir,

For plotMutationSpectrum function,I want to know the exact process of calculating contribution.

Regarding second question I have run the same code 10 times,please have a look at the link for the code https://www.dropbox.com/s/sug1i8v1zoqm1ce/Mutation_signature_package_data.R?dl=0

Please have a look at this link https://www.dropbox.com/s/p30pdl0a7ifdv7a/ss1_ss2.png?dl=0 where I have attached an image of two plots which are slightly different to each other. I have used this function

plotSignatures(sigs_nmf) + ggtitle("Somatic Signatures: NMF - Barchart") and run this 10 times on the dataset supplied with the package,the plot on the right side occurred 8 times whereas the plot on the left side occurred 2 times.

We have also run this for our dataset but the dissimilarity is more.

Thanks

Swati