lollipopPlot {maftools} | R Documentation |
Draws lollipop plot of amino acid changes.
lollipopPlot(maf, gene = NULL, AACol = NULL, labelPos = NULL, labPosSize = 3, showMutationRate = TRUE, fn = NULL, showDomainLabel = TRUE, cBioPortal = FALSE, refSeqID = NULL, proteinID = NULL, repel = FALSE, collapsePosLabel = TRUE, legendTxtSize = 10, labPosAngle = 0, domainLabelSize = 2.5, axisTextSize = c(9, 12), printCount = FALSE, colors = NULL, domainColors = NULL, labelOnlyUniqueDoamins = TRUE, defaultYaxis = TRUE, titleSize = c(12, 10), pointSize = 1.5)
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 3 |
showMutationRate |
Default TRUE |
fn |
basename for plot file to be saved. If provided a pdf will be generated. Default NULL. |
showDomainLabel |
Label domains within the plot. Default TRUE. If FALSE they will be annotated in legend. |
cBioPortal |
Adds annotations similar to cBioPortals MutationMapper and collapse Variants into Truncating and rest. |
refSeqID |
RefSeq transcript identifier for |
proteinID |
RefSeq protein identifier for |
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 |
legendTxtSize |
Text size for legend. Default 10 |
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 2. |
axisTextSize |
text size x and y tick labels. Default c(9,12). |
printCount |
If TRUE, prints number of summarized variants for the given protein. |
colors |
named vector of colors for each Variant_Classification. Default NULL. |
domainColors |
Manual colors for protein domains |
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(12, 10) |
pointSize |
size of lollipop heads. Default 1.5 |
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.
ggplot object of the plot, which can be futher modified.
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')