lollipopPlot2 {maftools} | R Documentation

## Compare two lollipop plots

### Description

Compare two lollipop plots

### Usage

    lollipopPlot2(
      m1,
      m2,
      gene = NULL,
      AACol1 = NULL,
      AACol2 = NULL,
      m1_name = NULL,
      m2_name = NULL,
      m1_label = NULL,
      m2_label = NULL,
      refSeqID = NULL,
      proteinID = NULL,
      labPosAngle = 0,
      labPosSize = 0.9,
      colors = NULL,
      alpha = 1,
      axisTextSize = c(1, 1),
      pointSize = 1.2,
      roundedRect = TRUE,
      showDomainLabel = TRUE,
      domainBorderCol = "black",
      domainLabelSize = 1,
      legendTxtSize = 1,
      verbose = TRUE
    )

### Arguments

`m1` | first `MAF` object
`m2` | second `MAF` object
`gene` | HGNC symbol for which protein structure to be drawn.
`AACol1` | manually specify column name for amino acid changes in m1. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'.
`AACol2` | manually specify column name for amino acid changes in m2. Default looks for fields 'HGVSp_Short', 'AAChange' or 'Protein_Change'.
`m1_name` | name for `m1` cohort. optional.
`m2_name` | name for `m2` cohort. optional.
`m1_label` | Amino acid positions to label for `m1` cohort. If 'all', labels all variants.
`m2_label` | Amino acid positions to label for `m2` cohort. If 'all', labels all variants.
`refSeqID` | RefSeq transcript identifier for `gene` if known.
`proteinID` | RefSeq protein identifier for `gene` if known.
`labPosAngle` | angle for labels. Defaults to horizonal 0 degree labels. Set to 90 for vertical; 45 for diagonal labels.
`labPosSize` | Text size for labels. Default 3
`colors` | named vector of colors for each Variant_Classification. Default NULL.
`alpha` | color adjustment. Default 1
`axisTextSize` | text size for axis labels. Default 1.
`pointSize` | size of lollipop heads. Default 1.2
`roundedRect` | Default FALSE. If 'TRUE' domains are drawn with rounded corners. Requires `berryFunctions`
`showDomainLabel` | Label domains within the plot. Default TRUE. If FALSE domains are annotated in legend.
`domainBorderCol` | Default "black". Set to NA to remove.
`domainLabelSize` | text size for domain labels. Default 1.
`legendTxtSize` | Default 1.
`verbose` | Default TRUE

### Details

Draws lollipop plot for a gene from two cohorts

### Value

invisible list of domain overlaps

### See Also

`lollipopPlot`

`mafCompare`

### Examples

    primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
    relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
    primary.apl <- read.maf(maf = primary.apl)
    relapse.apl <- read.maf(maf = relapse.apl)
    lollipopPlot2(m1 = primary.apl, m2 = relapse.apl, gene = "FLT3",AACol1 = "amino_acid_change", AACol2 = "amino_acid_change", m1_name = "Primary", m2_name = "Relapse")

[Package maftools version 2.10.05 Index]