plothist | R Documentation |
Plot histogram to compare number of mutations.
plothist(X, X.class = NULL, Mu = NULL, fill.color = .Color,
draw.all = TRUE, main = "Mutation counts",
xlab = "Difference", ylab = "Counts", append = FALSE)
X |
nid/sid matrix with |
X.class |
class ids indicated for all sequences. |
Mu |
a central sequence with length |
fill.color |
color to fill the histogram. |
draw.all |
draw a histogram use all sequences. |
main |
main label, default = "Mutation counts". |
xlab |
x-axis label, default = "Difference". |
ylab |
y-axis label, default = "Counts". |
append |
overwrite histograms. |
If X.class
is set, the histograms will be drawn by classes and
all sequences will be compared to the central sequence Mu
.
Otherwise, all sequences will be used to count mutations.
draw.all
is not effect if X.class
is not set.
If Mu
is set, it will be used to compare to all other sequences
to count mutations. Otherwise, the first sequence of X
will be
used, and the first sequence in the first class will be used if
X.class
is set. If Mu
is a matrix, the first row will be
used as the central sequence.
Histograms will be drawn to show the number of mutations away from the central sequence.
Wei-Chen Chen wccsnow@gmail.com
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
seqgen
,
plotdots
.
## Not run:
library(phyclust, quiet = TRUE)
X <- seq.data.toy$org
plothist(X)
# With class ids
X.class <- as.numeric(gsub(".*-(.*)", "\\1", seq.data.toy$seqname))
plothist(X, X.class)
## End(Not run)
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