Description Usage Arguments Value Examples
A convenience function for creating volcano plot.
1 2 3 4 5 6 7 8 9 | volcano_plot(
logFC,
significance,
feature_names = NULL,
threshold = NULL,
top_n_names = 5,
scale_xy = 1,
...
)
|
logFC |
a numeric vector of log2 of fold change for each feature |
significance |
a numeric vector of significance values (p-value, q-value or adjusted p-value) |
feature_names |
a character vector with the names of the features to diplay or NULL (default) |
threshold |
a numeric value where to draw a significance threshold or NULL (default) |
top_n_names |
number of top significant features to show the names (default 5) |
scale_xy |
numeric controls the spread on x vs y axis. Default 1. |
... |
additional arguments passed to |
plot
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | library("vp.misc")
data("cptac_oca")
library("limma")
ee <- oca.set
ee <- ee[rowSums(!is.na(exprs(ee))) >= 30,]
model.string <- "~ PLATINUM.STATUS + AGE" # model with covariates
coef.string <- "PLATINUM.STATUS" # note, only two levels allowed here
res <- limma_a_b(oca.set,
model.str = "~ PLATINUM.STATUS + AGE",
coef.str = "PLATINUM.STATUS")
head(res)
#library(qvalue)
library(ggplot2)
# res <- subset(res, !is.na(res$P.Value))
#res$q.value <- qvalue(res$P.Value)$qvalue
volcano_plot(res$logFC,
res$P.Value,
feature_names = rownames(res),
threshold = 0.05,
top_n_names = sum(res$P.Value < 0.001, na.rm=TRUE),
rep.fact=10000, adj.lmt=1000, adj.max=1000) +
theme(text=element_text(size = 20)) +
ylab("p-value") +
xlab("log2 fold change")
|
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