search

PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
452 stars 222 forks source link

Lollipopplot does not show complete protein length. #1029

Closed Arnob5105 closed 2 months ago

Arnob5105 commented 5 months ago

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

lollipopPlot(
  maf = maffiles,
  gene = 'MUC3A',
  AACol = 'Protein_Change',
  showMutationRate = TRUE,
  showDomainLabel = FALSE,
  labPosSize = 1.2,
  printCount = TRUE,
  labPosAngle = 90,
  repel = FALSE,
  legendTxtSize = 1.4,
  axisTextSize = c(1.3,1.3),
  labelOnlyUniqueDoamins = FALSE,
  titleSize = c(1.4,1.2),
  pointSize = 1.8,
  domainLabelSize = 1.4
  )
PoisonAlien commented 5 months ago

Hi,

I don't know which transcript the length of 3323 corresponds to. As per cBioPortal - the length and transcript seems to match

Arnob5105 commented 5 months ago

Hi, thanks for your quick reply. But according to Uniprot, the length of the protein is 3323. Moreover, in our analysis we also got the same length and mutational site, which extends beyond 876 amino acids.

PoisonAlien commented 5 months ago

Could you please post the transcript ID?

Arnob5105 commented 4 months ago

It's ENST00000379458.9

github-actions[bot] commented 2 months ago

This issue is stale because it has been open for 60 days with no activity.

github-actions[bot] commented 2 months ago

This issue was closed because it has been inactive for 14 days since being marked as stale.