TCGAVisualize_volcano {TCGAbiolinks} | R Documentation |
Creates a volcano plot from the expression and methylation analysis.
TCGAVisualize_volcano(x, y, filename = "volcano.pdf", ylab = expression(paste(-Log[10], " (FDR corrected -P values)")), xlab = NULL, title = "Volcano plot", legend = NULL, label = NULL, xlim = NULL, ylim = NULL, color = c("black", "red", "green"), names = NULL, names.fill = TRUE, show.names = "significant", x.cut = 0, y.cut = 0.01, height = 5, width = 10, highlight = NULL, highlight.color = "orange", names.size = 4, dpi = 300)
x |
x-axis data |
y |
y-axis data |
filename |
Filename. Default: volcano.pdf, volcano.svg, volcano.png |
ylab |
y axis text |
xlab |
x axis text |
title |
main title. If not specified it will be "Volcano plot (group1 vs group2) |
legend |
Legend title |
label |
vector of labels to be used in the figure. Example: c("Not Significant","Hypermethylated in group1", "Hypomethylated in group1"))#' |
xlim |
x limits to cut image |
ylim |
y limits to cut image |
color |
vector of colors to be used in graph |
names |
Names to be ploted if significant. Should be the same size of x and y |
names.fill |
Names should be filled in a color box? Default: TRUE |
show.names |
What names will be showd? Possibilities: "both", "significant", "highlighted" |
x.cut |
x-axis threshold. Default: 0.0 If you give only one number (e.g. 0.2) the cut-offs will be -0.2 and 0.2. Or you can give diffenrent cutt-ofs as a vector (e.g. c(-0.3,0.4)) |
y.cut |
p-values threshold. |
height |
Figure height |
width |
Figure width |
highlight |
List of genes/probes to be highlighted. It should be in the names argument. |
highlight.color |
Color of the points highlighted |
names.size |
Size of the names text |
dpi |
Figure dpi |
Creates a volcano plot from the expression and methylation analysis. Please see the vignette for more information Observation: This function automatically is called by TCGAanalyse_DMR
Saves the volcano plot in the current folder
x <- runif(200, -1, 1) y <- runif(200, 0.01, 1) TCGAVisualize_volcano(x,y) ## Not run: TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=0.8, names = rep("AAAA",length(x)), legend = "Status", names.fill = FALSE) TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=0.8, names = as.character(1:length(x)), legend = "Status", names.fill = TRUE, highlight = c("1","2"),show="both") TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=c(-0.3,0.8), names = as.character(1:length(x)), legend = "Status", names.fill = TRUE, highlight = c("1","2"),show="both") ## End(Not run) while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}