Draw two oncoplots side by side for cohort comparision.
Draw two oncoplots side by side for cohort comparision.
coOncoplot( m1, m2, genes = NULL, m1Name = NULL, m2Name = NULL, clinicalFeatures1 = NULL, clinicalFeatures2 = NULL, annotationColor1 = NULL, annotationColor2 = NULL, annotationFontSize = 1.2, sortByAnnotation1 = FALSE, sortByAnnotation2 = FALSE, sampleOrder1 = NULL, sampleOrder2 = NULL, additionalFeature1 = NULL, additionalFeaturePch1 = 20, additionalFeatureCol1 = "white", additionalFeatureCex1 = 0.9, additionalFeature2 = NULL, additionalFeaturePch2 = 20, additionalFeatureCol2 = "white", additionalFeatureCex2 = 0.9, sepwd_genes1 = 0.5, sepwd_samples1 = 0.5, sepwd_genes2 = 0.5, sepwd_samples2 = 0.5, colors = NULL, removeNonMutated = TRUE, anno_height = 2, legend_height = 4, geneNamefont = 0.8, showSampleNames = FALSE, SampleNamefont = 0.5, barcode_mar = 1, outer_mar = 3, gene_mar = 1, legendFontSize = 1.2, titleFontSize = 1.5, keepGeneOrder = FALSE, bgCol = "#CCCCCC", borderCol = "white" )
m1 |
first |
m2 |
second |
genes |
draw these genes. Default plots top 5 mutated genes from two cohorts. |
m1Name |
optional name for first cohort |
m2Name |
optional name for second cohort |
clinicalFeatures1 |
columns names from 'clinical.data' slot of m1 |
clinicalFeatures2 |
columns names from 'clinical.data' slot of m2 |
annotationColor1 |
list of colors to use for 'clinicalFeatures1' Default NULL. |
annotationColor2 |
list of colors to use for 'clinicalFeatures2' Default NULL. |
annotationFontSize |
font size for annotations Default 1.2 |
sortByAnnotation1 |
logical sort oncomatrix (samples) by provided 'clinicalFeatures1'. Sorts based on first 'clinicalFeatures1'. Defaults to FALSE. column-sort |
sortByAnnotation2 |
same as above but for m2 |
sampleOrder1 |
Manually speify sample names in m1 for oncolplot ordering. Default NULL. |
sampleOrder2 |
Manually speify sample names in m2 for oncolplot ordering. Default NULL. |
additionalFeature1 |
a vector of length two indicating column name in the MAF and the factor level to be highlighted. |
additionalFeaturePch1 |
Default 20 |
additionalFeatureCol1 |
Default "white" |
additionalFeatureCex1 |
Default 0.9 |
additionalFeature2 |
a vector of length two indicating column name in the MAF and the factor level to be highlighted. |
additionalFeaturePch2 |
Default 20 |
additionalFeatureCol2 |
Default "white" |
additionalFeatureCex2 |
Default 0.9 |
sepwd_genes1 |
Default 0.5 |
sepwd_samples1 |
Default 0.5 |
sepwd_genes2 |
Default 0.5 |
sepwd_samples2 |
Default 0.5 |
colors |
named vector of colors for each Variant_Classification. |
removeNonMutated |
Logical. If |
anno_height |
Height of clinical margin. Default 2 |
legend_height |
Height of legend margin. Default 4 |
geneNamefont |
font size for gene names. Default 1 |
showSampleNames |
whether to show sample names. Defult FALSE. |
SampleNamefont |
font size for sample names. Default 0.5 |
barcode_mar |
Margin width for sample names. Default 1 |
outer_mar |
Margin width for outer. Default 3 |
gene_mar |
Margin width for gene names. Default 1 |
legendFontSize |
font size for legend. Default 1.2 |
titleFontSize |
font size for title. Default 1.5 |
keepGeneOrder |
force the resulting plot to use the order of the genes as specified. Default FALSE |
bgCol |
Background grid color for wild-type (not-mutated) samples. Default gray - "#CCCCCC" |
borderCol |
border grid color for wild-type (not-mutated) samples. Default 'white' |
Draws two oncoplots side by side to display difference between two cohorts.
Returns nothing. Just draws plot.
#' ##Primary and Relapse APL
primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
##Read mafs
primary.apl <- read.maf(maf = primary.apl)
relapse.apl <- read.maf(maf = relapse.apl)
##Plot
coOncoplot(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary APL', m2Name = 'Relapse APL')
dev.off()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.