coOncoplot {maftools} | R Documentation |
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, sortByAnnotation1 = FALSE, sortByAnnotation2 = FALSE, colors = NULL, removeNonMutated = TRUE, geneNamefont = 10, showSampleNames = FALSE, SampleNamefont = 10, legendFontSize = 10, titleFontSize = 12, keepGeneOrder = FALSE, includeSyn = FALSE, bgCol = "#CCCCCC", borderCol = NA)
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. |
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 |
colors |
named vector of colors for each Variant_Classification. |
removeNonMutated |
Logical. If |
geneNamefont |
font size for gene names. Default 10 |
showSampleNames |
whether to show sample names. Defult FALSE. |
SampleNamefont |
font size for sample names. Default 10 |
legendFontSize |
font size for legend. Default 10 |
titleFontSize |
font size for title. Default 12 |
keepGeneOrder |
force the resulting plot to use the order of the genes as specified. Default FALSE |
includeSyn |
Set to TRUE to include silent variants. 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 NA. |
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()