maftools

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Feature suggestion: Add sample names to TMB plot

1

Hi! Thank you for providing this fantastic package 🤩 I am currently using maftools 2.10.0. I have been using the `tmb()` plot. From reading through the manual it doesn't seem...

FriederikeHanssen

I would like to be able to reverse the colors used with somaticInteractions. I use the option colPal = 'RdBu'. I would like the Co-occurence to be in red and...

lflechon

t_vaf is not included in my merged mag object, so I wanted to calculate it using the formula below. However, the column that is being created is not recognised by...

MjelleLab

is there a ref.build I can use for mouse data (mm10)?

FerTalavera

Lollipop plots

3

Hi I created nice lollipop plot using maftools. The issue is I facing difficulty creating a scale on Y-axis. Here is my code: ```r lollipopPlot( maf = laml, gene =...

shhabnsbwjd

extra space somaticInteractions

1

**Describe the issue** A clear and concise description of what the issue is. There is extra space **Command** Please post your commands and the output (errors or any unexpected output)...

xiw588

Plot is being masked by a white layer

2

I am trying with TCGA-LUSC data, and when tried to plot oncoplot, it appears like this: [oncoplot_luad.pdf](https://github.com/PoisonAlien/maftools/files/14305269/oncoplot_luad.pdf) It appears that there is a white layer has been appended on top...

manwarA

Hello, I am trying to filter my variants based on population allele frequency with subsetMaf, but I cannot figure out how to keep all those variants without a value for...

xguijarro

Question about gisticChromPlot

4

Hello, I have successfully ran GISTIC2 in canine data, and managed to get gisticChromPlot to generate a plot. However, the dog has 38 chromosomes, and the plot only shows the...

AnnaDvdH

Lollipopplot does not show complete protein length.

4

**Describe the issue** We tried to plot "MUC3A" in lollipop plot. The length of the actual protein is 3323 according to uniprot database. But it is only showing 876. **Command**...

Arnob5105