Description Usage Arguments Details Value Examples
Draws lollipop plot of amino acid changes. Protein domains are derived from PFAM database.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | 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 |
an |
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 'FALSEā 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
1 2 3 | 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')
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.