lollipopPlot {maftools} | R Documentation

## Draws lollipop plot of amino acid changes on to Protein structure.

### Description

Draws lollipop plot of amino acid changes. Protein domains are derived from PFAM database.

### Usage

    lollipopPlot(
      maf,
      gene = NULL,
      AACol = NULL,
      labelPos = NULL,
      labPosSize = 0.9,
      showMutationRate = TRUE,
      showDomainLabel = TRUE,
      cBioPortal = FALSE,
      refSeqID = NULL,
      proteinID = NULL,
      roundedRect = TRUE,
      repel = FALSE,
      collapsePosLabel = TRUE,
      showLegend = TRUE,
      legendTxtSize = 0.8,
      labPosAngle = 0,
      domainLabelSize = 0.8,
      axisTextSize = c(1, 1),
      printCount = FALSE,
      colors = NULL,
      domainAlpha = 1,
      domainBorderCol = "black",
      bgBorderCol = "black",
      labelOnlyUniqueDoamins = TRUE,
      defaultYaxis = FALSE,
      titleSize = c(1.2, 1),
      pointSize = 1.5
    )

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`gene` | HGNC symbol for which protein structure to be drawn.
`AACol` | manually specify column name for amino acid changes. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'. Changes can be of any format i.e, can be a numeric value or HGVSp annotations (e.g; p.P459L, p.L2195Pfs*30 or p.Leu2195ProfsTer30)
`labelPos` | Amino acid positions to label. If 'all', labels all variants.
`labPosSize` | Text size for labels. Default 0.9
`showMutationRate` | Whether to show the somatic mutation rate on the title. Default TRUE
`showDomainLabel` | Label domains within the plot. Default TRUE. If 'FALSE“ domains are annotated in legend.
`cBioPortal` | Adds annotations similar to cBioPortals MutationMapper and collapse Variants into Truncating and rest.
`refSeqID` | RefSeq transcript identifier for `gene` if known.
`proteinID` | RefSeq protein identifier for `gene` if known.
`roundedRect` | Default TRUE. If 'TRUE' domains are drawn with rounded corners. Requires `berryFunctions`
`repel` | If points are too close to each other, use this option to repel them. Default FALSE. Warning: naive method, might make plot ugly in case of too many variants!
`collapsePosLabel` | Collapses overlapping labels at same position. Default TRUE
`showLegend` | Default TRUE
`legendTxtSize` | Text size for legend. Default 0.8
`labPosAngle` | angle for labels. Defaults to horizonal 0 degree labels. Set to 90 for vertical; 45 for diagonal labels.
`domainLabelSize` | text size for domain labels. Default 0.8
`axisTextSize` | text size x and y tick labels. Default c(1,1).
`printCount` | If TRUE, prints number of summarized variants for the given protein.
`colors` | named vector of colors for each Variant_Classification. Default NULL.
`domainAlpha` | Default 1
`domainBorderCol` | Default "black". Set to NA to remove.
`bgBorderCol` | Default "black". Set to NA to remove.
`labelOnlyUniqueDoamins` | Default TRUE only labels unique doamins.
`defaultYaxis` | If FALSE, just labels min and maximum y values on y axis.
`titleSize` | font size for title and subtitle. Default c(1.2, 1)
`pointSize` | size of lollipop heads. Default 1.5

### Details

This function by default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change' in maf file. One can also manually specify field name containing amino acid changes.

### Value

Nothing

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    lollipopPlot(maf = laml, gene = 'KIT', AACol = 'Protein_Change')

[Package maftools version 2.6.05 Index]