Draws lollipop plot of amino acid changes on to Protein structure.
Draws lollipop plot of amino acid changes. Protein domains are derived from PFAM database.
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 )
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 |
proteinID |
RefSeq protein identifier for |
roundedRect |
Default TRUE. If 'TRUE' domains are drawn with rounded corners. Requires |
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 |
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.
Nothing
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')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.