plot.landscape2: Visualize mutation landscape

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

A function to plot mutational landscape of significantly mutated genes.

Usage

plot.landscape2(upper.panel, middle.panel, left.panel, right.panel, legend.panel, subtype.panel=NULL, subtype.2.panel=NULL,
    output.fig.pdffile=NULL,
    left.panel.xlim=NULL,
    family.font="sans", 
    syn.nonsyn.legend.color=NULL,
    syn.nonsyn.legend.ncol=NULL,
    syn.nonsyn.legend.loc="top",
    image.color=NULL,

    subtype.labels=NULL,
    subtype.label.cex=1,
    subtype.panel.color=brewer.pal(7, "Dark2"),
    subtype.panel.identifier="",                        # subtype identifier, e.g. Lauren's subtype, Clonality status
    subtype.panel.identifier.cex=0.6,                   # cex for subtype identifier
    subtype.legend.text.width=NULL,                     # text.width passed to legend(...) to adjust distances between 2 adjacent legend strings

	subtype.2.labels=NULL,
    subtype.2.label.cex=1,
    subtype.2.panel.color=brewer.pal(7, "Set2"),
    subtype.2.panel.identifier="",                      # subtype identifier, e.g. Lauren's subtype, Clonality status
    subtype.2.panel.identifier.cex=0.6,                 # cex for subtype identifier
    subtype.2.legend.text.width=NULL,                   # text.width passed to legend(...) to adjust distances between 2 adjacent legend strings

    right.panel.color=brewer.pal(7, "Purples")[5],
    sort.by.qvalue=FALSE,
    group.by.subtype=FALSE,
    left.panel.cex.axis=1.5,
    right.panel.cex.axis=1.3,
    upper.panel.mar=c(0.2, 1.3, 0.5, 1.16),
    legend.panel.mar=c(0, 1, 2, 1),
    legend.panel.ncol=NULL,
    legend.panel.y=-0.05,
    left.panel.mar=c(5.5, 1.5, 0.2, 2.9),
    middle.panel.mar=c(5.5, 1.3, 0.2, 1.16),
    right.panel.mar=c(5.5, 3, 0.2, 1.5),
    left.panel.xlab="Individuals\nwith mutations",
    left.panel.xlab.cex=1,
    right.panel.xlab="-log10\n(q-value)",
    right.panel.xlab.cex=1,
    right.panel.qscore.cutoff=1,
    right.panel.qscore.lwd=0.5,
    right.panel.qscore.lty='dashed',
    right.panel.qscore.col='red')

Arguments

upper.panel	A data frame for upper panel barplot, see details for detail description of file format.
middle.panel	A matrix for middle panel, attached with row and col names, see details for detail description of file format.
left.panel	A data frame for the left panel, see details for detail description of file format.
right.panel	A data frame for the left panel, see details for detail description of file format.
legend.panel	A data frame contains information about mutation type mapping.
subtype.panel	The main subtype panel, a data frame of sample sutbypes, 1st col is sample name, whereas 2nd col is subtype.
subtype.2.panel	The 2nd subtype panel, a data frame of sample sutbypes, 1st col is sample name, whereas 2nd col is subtype.
output.fig.pdffile	figure file name, ended with .pdf.
subtype.labels	text labels for sample subtypes, e.g. Intestinal and Diffuse.
subtype.2.labels	text labels for sample subtypes, e.g. Intestinal and Diffuse.
group.by.subtype	if TRUE, group samples by subtypes.
syn.nonsyn.legend.color	A vector of 2 elements indicating colors used for syn. and non-syn. mutations.
syn.nonsyn.legend.ncol	ncol passes to legend(...).
syn.nonsyn.legend.loc	Legend location, e.g. top, right etc.
image.color	A vector of elements representing different mutation types.
subtype.panel.color	A vector representing colors used for subtypes.
right.panel.color	Color for barplot on the right panel.
sort.by.qvalue	Sort right panel data frame according to q-value.
left.panel.xlim	xlim for left panel.
family.font	font family used set in par(family=family.font).
left.panel.cex.axis	cex.axis for the left panel at side=4, control the size of percentage.
right.panel.cex.axis	cex.axis for right panel at side=1, control the size of gene names.
upper.panel.mar	mar in par(mar=c(...)) for upper panel.
legend.panel.mar	mar in par(mar=c(...)) for top right legend panel.
legend.panel.ncol	ncol passes to legend(...).
legend.panel.y	Y coordinate for legend.panel.
left.panel.mar	mar in par(mar=c(...)) for left panel.
middle.panel.mar	mar in par(mar=c(...)) for middle panel.
right.panel.mar	mar in par(mar=c(...)) for right panel.
legend.syn.nonsyn.x,legend.syn.nonsyn.y	set for top left legend via legend(x=legend.syn.nonsyn.x,y=legend.syn.nonsyn.y).
left.panel.xlab	left panel xlab.
left.panel.xlab.cex	cex for left panel xlab.
right.panel.xlab	right panel xlab.
right.panel.xlab.cex	cex for right panel xlab.
right.panel.qscore.cutoff	Q-score cutoff.
right.panel.qscore.lwd	lwd for qscore cutoff, set 0 to get rid of it.
right.panel.qscore.lty	lty for qscore cutoff.
right.panel.qscore.col	col for qscore cutoff.

Details

upper.panel has 3 columns, the 1st is sample names, the 2nd and 3rd are the number of silent and non-silent mutations, e.g. *Note:It's highly recommended NOT to include '-' in sample names

sample silence nonsilence
GC03_T 167 551
GC10_T 179 471
GC04_T 160 388
GC05_T 156 391

middle.panel is a matrix, attached with row and columns, e.g.

GC118_T GC191_T GC178_T GC101_T
TP53 0 0 0 0
ARID1A 0 0 2 0
CDH1 6 0 0 3
PTK2B 0 0 0 0
RPL22 0 0 5 0
BAX 0 0 0 0
CYC1 0 0 0 0
KRAS 0 0 0 0
ITGAV 0 0 0 0
HIST1H2AD 0 0 3 0

left.panel is a data frame with 3 columns, e.g.

gene nonsilence_sample_num nonsilent_sample_percent
TP53 45 37.2%
ARID1A 28 23.1%
CDH1 21 17.4%
PTK2B 17 14.0%
RPL22 12 9.9%
BAX 11 9.1%

right.panel is a data frame with 2 columns, e.g.

gene q
TP53 1.73999e-07
ARID1A 0.002062569
CDH1 2.875046e-06
PTK2B 0.001464807
RPL22 1.73999e-07
BAX 1.73999e-07

legend.panel is a data frame with 2 columns, e.g.

7 Nonsense
6 Splice site
5 Frame shift
4 Inframe indel
3 Missense
2 Syn.

You can also use the pre-specified image color as:

data("LandscapeColor")
ls()

See Also

plot.depth,plot.MH

Examples

library(RColorBrewer)
data("SMG", package="lxctk")
data("LandscapeColor")

plot.landscape2(upper.panel, middle.panel, left.panel, right.panel, legend.panel, subtype.panel, subtype.labels=c('Intestinal','Diffuse'), image.color=image.color.lixc)

# Use different color scheme
plot.landscape2(upper.panel, middle.panel, left.panel, right.panel, legend.panel, subtype.panel, subtype.labels=c('Intestinal','Diffuse'), image.color=image.color.Set2)


plot.landscape2(upper.panel, middle.panel, left.panel, right.panel, legend.panel, subtype.panel, subtype.labels=c('Intestinal','Diffuse'),output.fig.pdffile="GastricCancer.SMG.Landscape.pdf")

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.