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
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot_enrichment_depletion.R
\name{plot_enrichment_depletion}
\alias{plot_enrichment_depletion}
\title{Plot enrichment/depletion of mutations in genomic regions}
\usage{
plot_enrichment_depletion(df, sig_type = c("fdr", "p"))
}
\arguments{
\item{df}{Dataframe result from enrichment_depletion_test()}
\item{sig_type}{The type of significance to be used. Possible values:
* 'fdr' False discovery rate.
A type of multiple testing correction.;
* 'p' for regular p values.}
}
\value{
Plot with two parts. 1: Barplot with no. mutations expected and
observed per region. 2: Effect size of enrichment/depletion
(log2ratio) with results significance test.
}
\description{
Plot enrichment/depletion of mutations in genomic regions
}
\examples{
## See the 'genomic_distribution()' example for how we obtained the
## following data:
distr <- readRDS(system.file("states/distr_data.rds",
package = "MutationalPatterns"
))
tissue <- c(
"colon", "colon", "colon",
"intestine", "intestine", "intestine",
"liver", "liver", "liver"
)
## Perform the enrichment/depletion test.
distr_test <- enrichment_depletion_test(distr, by = tissue)
## Plot the enrichment/depletion
plot_enrichment_depletion(distr_test)
#Perform and plot the enrichmet depletion test for all samples pooled
distr_test2 <- enrichment_depletion_test(distr)
plot_enrichment_depletion(distr_test2)
## Plot with p values instead of fdr
plot_enrichment_depletion(distr_test, sig_type = "p")
## Use multiple (max 3) significance cutoffs.
## This will vary the number of significance stars.
distr_multistars <- enrichment_depletion_test(distr,
by = tissue,
p_cutoffs = c(0.05, 0.01, 0.005),
fdr_cutoffs = c(0.1, 0.05, 0.01)
)
plot_enrichment_depletion(distr_multistars)
}
\seealso{
\code{\link{enrichment_depletion_test}},
\code{\link{genomic_distribution}}
}
|
