Mutational landscape plot

Question

[shivangi.agarwal800]

Hi I am trying to make waterfall plot using GenVisR as shown here. I just put an example data like

sample           gene_name  amino.acid.change  trv_type
TCGA-BH-A0WA-01  BRCA1      X1559_splice       splice_site_del
TCGA-AN-A0XU-01  BRCA1      G1788V             missense
TCGA-A2-A25B-01  BRCA1      E720*              nonsense
TCGA-D8-A27M-01  BRCA1      P1614Qfs*19        frame_shift_del
TCGA-E9-A1NC-01  BRCA1      Q139*              nonsense
TCGA-C8-A12T-01  BRCA1      D1344H             missense
TCGA-A2-A4S0-01  BRCA1      K50T               missense
TCGA-LL-A5YP-01  BRCA1      D96H               missense
TCGA-PE-A5DE-01  BRCA1      E1419K             missense
TCGA-A1-A0SI-01  BRCA1      E9Q                missense
TCGA-AO-A1KR-01  BRCA1      C644del            in_frame_del
TCGA-E2-A1L9-01  BRCA1      S1027I             missense
TCGA-EW-A2FR-01  BRCA1      D366N              missense

and getting plot as shown here:

But in that, I did not understand how it is plotting translational effect, because there is no information regarding synonymous or non-synonyms mutations.

[WouterDeCoster]

How to add images to a Biostars post

[WouterDeCoster]

A missense or indel variant is non-synonymous, and that information is in your table.

[shivangi.agarwal800]

But, in this case, its not like that, all missense mutations are not non-synonyms.

[WouterDeCoster]

all missense mutations are not non-synonyms

A missense variant is by definition non-synonymous.

[shivangi.agarwal800]

Ok, I got it. That is fine. But, among non-synonyms, if we want to indicate the lethal mutation in the plot itself, how it can be done?

[Devon Ryan]

What do you mean by "lethal" mutations? That's not a standard classification.

[shivangi.agarwal800]

It means that the mutations having deleterious functional impact. It is not a standard classification, but it can be predicted using different tools. I got the information from cbioportal. My concern is if we can show these mutations in the graph itself while giving its information in input file.

Answer 1

[Devon Ryan]

You need to annotated these using something like Ensembl's variant effect predictor (there are a number of alternatives to this).

[shivangi.agarwal800]

That is fine, but I need to plot these in waterfall plot itself. Can it be done?

[Devon Ryan]

You have to label them before you can plot them.

[shivangi.agarwal800]

Hi

I noticed one problem while plotting this plot. When I simply plotted data given in the link, I noticed that the gene which is having two same types of mutation with different variant in the same sample is being shown in the plot only once. example, the gene MAP3K1 is having two frame shift mutations, as p.H1058fs and p.I1218fs in sample 12, the plot shows only first one, and not showing second mutation. The plot is shown here:

    12  MAP3K1  frame_shift_ins p.H1058fs
    12  MAP3K1  frame_shift_ins p.I1218fs

Why it is so? Is there any other code to add to plot both one. Please suggest.
Thanks in advance.

[Devon Ryan]

Ask Obi, it's his tool.