dotplot.phylo4d | R Documentation |
Dotplot of Traits Values along a Phylogeny
## S3 method for class 'phylo4d'
dotplot(
p4d,
trait = names(tdata(p4d)),
center = TRUE,
scale = TRUE,
tree.ladderize = FALSE,
tree.type = "phylogram",
tree.ratio = NULL,
tree.xlim = NULL,
tree.open.angle = 0,
tree.open.crown = TRUE,
show.tip = TRUE,
tip.labels = NULL,
tip.col = "black",
tip.cex = 1,
tip.font = 3,
tip.adj = 0,
data.xlim = NULL,
show.data.axis = TRUE,
dot.col = "black",
dot.pch = 20,
dot.cex = 2,
show.trait = TRUE,
trait.labels = NULL,
trait.col = "black",
trait.cex = 1,
trait.font = 1,
trait.bg.col = "grey90",
error.bar.sup = NULL,
error.bar.inf = NULL,
error.bar.col = 1,
show.box = FALSE,
grid.vertical = FALSE,
grid.horizontal = TRUE,
grid.col = "grey25",
grid.lty = "dashed",
...
)
p4d |
a |
trait |
the traits in the |
center |
a logical indicating whether traits values should be centered. |
scale |
a logical indicating whether traits values should be scaled. |
tree.ladderize |
a logical indicating whether the tree should be (right) ladderized. |
tree.type |
a character string specifying the type of phylogeny to be drawn.
Can be " |
tree.ratio |
a numeric value in [0, 1] giving the proportion of width of the figure for the tree. |
tree.xlim |
a numeric vector of length 2 giving the limits of the x-axis for the tree. If |
tree.open.angle |
a numeric value giving the angle in degrees left blank if |
tree.open.crown |
a logical indicating whether the crowns should be drawn following the value
of |
show.tip |
logical indicating whether tips labels should be drawn. |
tip.labels |
character vector to label the tips.
If |
tip.col |
a vector of R colors to use for the tips labels. Recycled if necessary. |
tip.cex |
a numeric vector to control character size of the tips labels. Recycled if necessary. |
tip.font |
an integer vector specifying the type of font for the tips labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary. |
tip.adj |
a vector of numeric in [0, 1] to control tips labels justification: 0 (left-justification), 0.5 (centering), or 1 (right-justification). Recycled if necessary. |
data.xlim |
numeric vector of length 2 or matrix giving the x coordinates range for the barplots/dotplots (see Details). |
show.data.axis |
logical indicating whether barplots/dotplots axes should be drawn. |
dot.col |
a vector of R colors to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |
dot.pch |
a numerical vector of symbol to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |
dot.cex |
a numerical vector. Character (or symbol) expansion for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |
show.trait |
logical indicating whether traits labels should be drawn. |
trait.labels |
character vector to label the traits.
If |
trait.col |
a vector of R colors to use for the traits labels. Recycled if necessary. |
trait.cex |
a numeric vector to control character size of the trait labels. Recycled if necessary. |
trait.font |
an integer vector specifying the type of font for the traits labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary. |
trait.bg.col |
a vector of R colors to use for the background of the barplots. Recycled if necessary. |
error.bar.sup |
a matrix giving the superior limit for error bars. Columns and rows names must match with traits and tips labels, respectively. |
error.bar.inf |
a matrix giving the inferior limit for error bars. Columns and rows names must match with traits and tips labels, respectively. |
error.bar.col |
a vector of R colors to use for the bars. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |
show.box |
a logical indicating whether a box should be drawn around the plots. |
grid.vertical |
a logical incating whether vertical lines of the grid should be drawn. |
grid.horizontal |
a logical incating whether horizontal lines of the grid should be drawn. |
grid.col |
a vector of R colors to use for the lines of the grid. |
grid.lty |
the lines type of the grid. Possibly a vector. |
... |
further arguments to be passed to |
data(navic)
dotplot(navic)
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