oncoplot {maftools} | R Documentation |
takes output generated by read.maf and draws an oncoplot
oncoplot(maf, top = 20, genes = NULL, mutsig = NULL, mutsigQval = 0.1, drawRowBar = TRUE, drawColBar = TRUE, includeColBarCN = TRUE, draw_titv = FALSE, logColBar = FALSE, clinicalFeatures = NULL, exprsTbl = NULL, additionalFeature = NULL, additionalFeaturePch = 20, additionalFeatureCol = "white", additionalFeatureCex = 0.9, annotationDat = NULL, annotationColor = NULL, genesToIgnore = NULL, showTumorSampleBarcodes = FALSE, removeNonMutated = TRUE, fill = FALSE, colors = NULL, sortByMutation = FALSE, sortByAnnotation = FALSE, numericAnnoCol = NULL, groupAnnotationBySize = TRUE, annotationOrder = NULL, keepGeneOrder = FALSE, GeneOrderSort = TRUE, sampleOrder = NULL, writeMatrix = FALSE, fontSize = 0.8, SampleNamefontSize = 1, showTitle = TRUE, titleFontSize = 1.5, legendFontSize = 1.2, annotationFontSize = 1.2, bgCol = "#CCCCCC", borderCol = "white", colbar_pathway = FALSE)
maf |
|
top |
how many top genes to be drawn. defaults to 20. |
genes |
Just draw oncoplot for these genes. Default NULL. |
mutsig |
Mutsig resuts if availbale. Usually file named sig_genes.txt If provided plots significant genes and correpsonding Q-values as side row-bar. Default NULL. |
mutsigQval |
Q-value to choose significant genes from mutsig results. Default 0.1 |
drawRowBar |
logical plots barplot for each gene. Default |
drawColBar |
logical plots barplot for each sample. Default |
includeColBarCN |
Whether to include CN in column bar plot. Default TRUE |
draw_titv |
logical Includes TiTv plot. |
logColBar |
Plot top bar plot on log10 scale. Default |
clinicalFeatures |
columns names from 'clinical.data' slot of |
exprsTbl |
Expression values if availble. Must be a data.frame with two columns containing to gene names and expression values. |
additionalFeature |
a vector of length two indicating column name in the MAF and the factor level to be highlighted. |
additionalFeaturePch |
Default 20 |
additionalFeatureCol |
Default "white" |
additionalFeatureCex |
Default 0.9 |
annotationDat |
If MAF file was read without clinical data, provide a custom |
annotationColor |
Custom colors to use for 'clinicalFeatures'. Must be a named list containing a named vector of colors. Default NULL. See example for more info. |
genesToIgnore |
do not show these genes in Oncoplot. Default NULL. |
showTumorSampleBarcodes |
logical to include sample names. |
removeNonMutated |
Logical. If |
fill |
Logical. If |
colors |
named vector of colors for each Variant_Classification. |
sortByMutation |
Force sort matrix according mutations. Helpful in case of MAF was read along with copy number data. Default FALSE. |
sortByAnnotation |
logical sort oncomatrix (samples) by provided 'clinicalFeatures'. Sorts based on first 'clinicalFeatures'. Defaults to FALSE. column-sort |
numericAnnoCol |
color palette used for numeric annotations. Default 'YlOrBr' from RColorBrewer |
groupAnnotationBySize |
Further group 'sortByAnnotation' orders by their size. Defaults to TRUE. Largest groups comes first. |
annotationOrder |
Manually specify order for annotations. Works only for first 'clinicalFeatures'. Default NULL. |
keepGeneOrder |
logical whether to keep order of given genes. Default FALSE, order according to mutation frequency |
GeneOrderSort |
logical this is applicable when 'keepGeneOrder' is TRUE. Default TRUE |
sampleOrder |
Manually speify sample names for oncolplot ordering. Default NULL. |
writeMatrix |
writes character coded matrix used to generate the plot to an output file. |
fontSize |
font size for gene names. Default 0.8. |
SampleNamefontSize |
font size for sample names. Default 1 |
showTitle |
Default TRUE |
titleFontSize |
font size for title. Default 1.5 |
legendFontSize |
font size for legend. Default 1.2 |
annotationFontSize |
font size for annotations. Default 1.2 |
bgCol |
Background grid color for wild-type (not-mutated) samples. Default gray - "#CCCCCC" |
borderCol |
border grid color (not-mutated) samples. Default 'white'. |
colbar_pathway |
Draw top column bar with respect to diplayed pathway. Default FALSE. Not implemented yet! |
Takes maf file as input and plots it as a matrix. Any desired clincal features can be added at the bottom of the oncoplot by providing clinicalFeatures
.
Oncoplot can be sorted either by mutations or by clinicalFeatures using arguments sortByMutation
and sortByAnnotation
respectively.
None.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') laml <- read.maf(maf = laml.maf, clinicalData = laml.clin) #Basic onocplot oncoplot(maf = laml, top = 3) #Changing colors for variant classifications (You can use any colors, here in this example we will use a color palette from RColorBrewer) col = RColorBrewer::brewer.pal(n = 8, name = 'Paired') names(col) = c('Frame_Shift_Del','Missense_Mutation', 'Nonsense_Mutation', 'Multi_Hit', 'Frame_Shift_Ins', 'In_Frame_Ins', 'Splice_Site', 'In_Frame_Del') #Color coding for FAB classification; try getAnnotations(x = laml) to see available annotations. fabcolors = RColorBrewer::brewer.pal(n = 8,name = 'Spectral') names(fabcolors) = c("M0", "M1", "M2", "M3", "M4", "M5", "M6", "M7") fabcolors = list(FAB_classification = fabcolors) oncoplot(maf = laml, colors = col, clinicalFeatures = 'FAB_classification', sortByAnnotation = TRUE, annotationColor = fabcolors)