coGisticChromPlot: Co-plot version of gisticChromPlot()

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Co-plot version of gisticChromPlot()

Description

Use two GISTIC object or/and two MAF objects to view a vertical arranged version of Gistic Chromosome plot results on the Amp or Del G-scores.

Usage

coGisticChromPlot(
  gistic1 = NULL,
  gistic2 = NULL,
  g1Name = "",
  g2Name = "",
  type = "Amp",
  markBands = TRUE,
  labelGenes = TRUE,
  gLims = NULL,
  maf1 = NULL,
  maf2 = NULL,
  mutGenes = NULL,
  mutGenes1 = NULL,
  mutGenes2 = NULL,
  fdrCutOff = 0.05,
  symmetric = TRUE,
  color = NULL,
  ref.build = "hg19",
  cytobandOffset = "auto",
  txtSize = 0.8,
  cytobandTxtSize = 1,
  mutGenesTxtSize = 0.6,
  rugTickSize = 0.1
)

Arguments

gistic1	first GISTIC object
gistic2	second GISTIC object
g1Name	the title of the left side
g2Name	the title of the right side
type	default 'Amp', c('Amp',"Del"), choose one to plot, only focal events are shown, 'Amp' only shows the Amplification events, and 'Del' only shows the Deletion events.
markBands	default TRUE, integer of length 1 or 2 or TRUE, mark cytoband names of the outer side of the plot
labelGenes	if you want to label some genes you are interested along the chromosome, set it to TRUE
gLims	Controls the G-score's axis limits. Default NULL.
maf1, maf2	if labelGenes==TRUE, you need to provide MAF object, the genes mutation info collected from the maf1 is shown on the left side, while maf2 on the right side. the genes selected are controled by the mutGenes or mutGenes1 or mutGenes1 parameter, see following.
mutGenes, mutGenes1, mutGenes2	default NULL, could be NULL, number, or character vector of gene symbols which match the corresponding MAF object's Hugo_Symbol column values. mutGenes controls both sides of the annotation, mutGenes1 controls only left side and corresponding data is extracted from to maf1, and mutGenes2 controls only right side annotation and corresponding to maf2. If 'NULL', extract the top 50 mutated genes from maf1 and maf2 seperatedly then annotate them on the left side (maf1 genes) and right side (maf2 genes). if integer, say N, only top N genes will be extracted seperately from maf1 and maf2. These two condition leads to different genes annotated on both sides. If character vector, then the genes have mutated in maf1 and maf2 will be annotated on both side of the figure which mean the two sides have the same list of genes. if mutGenes is not NULL and both mutGenes1 and mutGenes1 are NULL, then the auto set mutGenes1 = mutGenes2 = mutGenes.
fdrCutOff	default 0.05,only items with FDR < fdrCutOff will be colored as Amp or Del ( colored 'Red' or 'Blue'), others will be seen as non-significant events (colored gray)
symmetric	default TRUE, If False, when the gistic1 and gistic2 have different max values of G-scores, the Chrom (0 point of x axis) will not be in the center of the whole plot, if you set symmetric==TRUE, then the one with smaller max(G-score) will be stretched larger to make the 0 of the x axis in the middle which eventually make the plot more symmetric.
color	NULL or a named vector. the color of the G-score lines, default NULL which will set the color c(Amp = "red", Del = "blue", neutral = 'gray70')
ref.build	default "hg19", c('hg18','hg19','hg38') supported at current.
cytobandOffset	default 'auto', the width of the chromosome rects (Y axis at 0 point of X axis). by default will be 0.015 of the width of the whole x axis length.
txtSize	the zoom value of most of the texts
cytobandTxtSize	textsize of the cytoband annotation
mutGenesTxtSize	textsize of the mutGenes annotation
rugTickSize	the rug line width of the cytoband annotation

Author(s)

bio_sun - https://github.com/biosunsci

Examples

## Not run: 
gistic_res_folder = system.file("extdata",package = "maftools")
laml.gistic = readGistic(gistic_res_folder)
laml.gistic2 = readGistic(gistic_res_folder)


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)
laml2 = laml

# --- plot ---
gisticChromPlot2v(gistic1 = laml.gistic, gistic2 = laml.gistic2, type='Del',
                   symmetric = TRUE, g1Name = 'TCGA1',
                   g2Name = 'TCGA2', maf1 = laml, maf2 = laml2, mutGenes = 30)

## End(Not run)

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.