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, axisTextSize = c(1, 1),
      pointSize = 1.2, domainLabelSize = 1, legendTxtSize = 1)

### 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.
`axisTextSize` | text size for axis labels. Default 1.
`pointSize` | size of lollipop heads. Default 1.2
`domainLabelSize` | text size for domain labels. Default 1.
`legendTxtSize` | Default 1.

### Details

Draws lollipop plot for a gene from two cohorts

### 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 1.8.0 Index]