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lollipopPlot2 - Structure for protein TTC40 not found

14

**Describe the issue** A clear and concise description of what the issue is. **Command** Please post your commands and the output (errors or any unexpected output) lollipopPlot2(m1 = AnnVarG, m2...

YingYa

Protein Structure not found

1

Hi there, I'm working on a project where we've generated tumours in mice and have sequenced it using WES. I'm attempting to visualize protein structure and mutations using lollipop plots....

vincentye2

Oncoplot gene bar sizes too small

1

**Describe the issue** Can't customize gene size bars, which make them too small! Even if I try sepwd_genes and sepwd_samples, nothing changes. Setting sepwd_genes to negative values increase the bar...

GACGAMA

No non-synonymous mutations found Check `vc_nonSyn`` argumet in `read.maf` for details

2

```r library(TCGAbiolinks) query_SNV

guohout

repel for plotOncodrive

1

Dear maftools-team, would it be possible to implement a repel argument in the plotOncodrive function for an easier visualisation? Thanks a lot for this package and your help! Best, Alexander

AlexanderPic

Using tcgaCompare() to plot mutation load between two cohorts

1

Hi Anand, Thank you for the tool! Would it be possible to generate a mutation load plot comparing two cohorts (rather than comparing one cohort to the 33 TCGA cohorts...

rajeha

Hi developers, I noticed some lines in this gistic2 are not straight, how can I change it? 

hfl112

trinucleotideMatrix function error

1

I have a MAF file generated using a version of the genome (GRCh38) which includes unplaced scaffolds. They are being ignored according to the trincleotideMatrix warning, but I'm still getting...

geejaytee

Oncoplot showing wrong mutations compared to orignal MAF file

3

**Describe the issue** So, I have selected top genes using MutSig2CV. I am passing the top genes in the "genes" parameter of oncoplot. But the color code generated in the...

dhwani2410

Hi. Thanks for the cool tool. I'm wondering if you can add some parameters to prepareMutSig so that it can add the effect and categ columns required by MutSigCV? Thanks.

lincj1994