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.

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??

Looking for your response.

Thanks

Swati

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.