VolcanoView {MAGeCKFlute} | R Documentation |
Volcano plot
VolcanoView(df, x = "logFC", y = "adj.P.Val", Label = NA, top = 5, topnames = NULL, x_cutoff = log2(1.5), y_cutoff = 0.05, mycolour = c("gray80", "#e41a1c", "#377eb8"), alpha = 0.6, main = NULL, xlab = "Log2 Fold Change", ylab = "-Log10(Adjust.P)", filename = NULL, width = 4, height = 2.5, ...)
df |
Data frame |
x |
Colname of df specifying x-axis in Volcanno figure, 'logFC' (default). |
y |
Colname of df specifying y-axis in Volcanno figure, 'adj.P.Val' (default), which will be plot after log10 transformation. |
Label |
Colname of df specifying labeled terms in Volcanno figure. |
top |
Interger, the number of top significant terms to be labeled. |
topnames |
Character vector, indicating interested terms to be labeled. |
x_cutoff |
Cutoff of x-axis. |
y_cutoff |
Cutoff of y-axis. |
mycolour |
A color vector, specifying colors of non-significant, significant up and down-regulated genes. |
alpha |
Parameter in ggplot. |
main |
Title of volcano figure. |
xlab |
Label of x-axis in figure. |
ylab |
Label of y-axis in figure. |
filename |
Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk. |
width |
Width of figure. |
height |
Height of figure. |
... |
Other available parameters in ggsave. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
data(rra.gene_summary) rra = ReadRRA(rra.gene_summary) VolcanoView(rra, x = "LFC", y = "FDR", Label = "Official")