| plotgaps {phyclust} | R Documentation |
This function provides gaps plots of data set to identify regions where gaps enriched. The plot show the proportions of context by sites and the diverse may be caused by mutations, sequencing errors, or alignment errors.
plotgaps(X, code.type = .code.type[1], main = "Gaps Plot",
xlab = "Sites", ylab = "Proportion", ...)
X |
numerical data matrix with N rows/sequences and L columns/sites. |
code.type |
either "NUCLEOTIDE" (default) or "SNP". |
main |
main label, default = "Gaps Plot". |
xlab |
x-axis label, default = "Sites". |
ylab |
y-axis label, default = "Proportion". |
... |
other options passed to |
Proportions of gaps will be drawn.
A gaps plot will be drawn.
Wei-Chen Chen wccsnow@gmail.com
Phylogenetic Clustering Website: http://snoweye.github.io/phyclust/
## Not run: library(phyclust, quiet = TRUE) # For nucleotide set.seed(1234) X <- seq.data.toy$org X[sample(c(T, F), length(X), replace = TRUE, prob = c(0.05, 0.95))] <- .nucleotide$nid[.nucleotide$code == "-"] plotgaps(X) ## End(Not run)