View source: R/dplot3_protein.R
dplot3_protein | R Documentation |
Plot the amino acid sequence with annotations
dplot3_protein(
x,
site = NULL,
region = NULL,
ptm = NULL,
clv = NULL,
variant = NULL,
disease.variants = NULL,
n.per.row = NULL,
main = NULL,
main.xy = c(0.055, 0.975),
main.xref = "paper",
main.yref = "paper",
main.xanchor = "middle",
main.yanchor = "top",
layout = c("simple", "grid", "1curve", "2curve"),
show.markers = TRUE,
show.labels = TRUE,
font.size = 18,
label.col = NULL,
scatter.mode = "markers+lines",
marker.size = 28,
marker.col = NULL,
marker.alpha = 1,
marker.symbol = "circle",
line.col = NULL,
line.alpha = 1,
line.width = 2,
show.full.names = TRUE,
region.scatter.mode = "markers+lines",
region.style = 3,
region.marker.size = marker.size,
region.marker.alpha = 0.6,
region.marker.symbol = "circle",
region.line.dash = "solid",
region.line.shape = "line",
region.line.smoothing = 1,
region.line.width = 1,
region.line.alpha = 0.6,
theme = rtTheme,
region.palette = rtPalette,
region.outline.only = FALSE,
region.outline.pad = 2,
region.pad = 0.35,
region.fill.alpha = 0.1666666,
region.fill.shape = "line",
region.fill.smoothing = 1,
bpadcx = 0.5,
bpadcy = 0.5,
site.marker.size = marker.size,
site.marker.symbol = marker.symbol,
site.marker.alpha = 1,
site.border.width = 1.5,
site.palette = rtPalette,
variant.col = "#FA6E1E",
disease.variant.col = "#E266AE",
showlegend.ptm = TRUE,
ptm.col = NULL,
ptm.symbol = "circle",
ptm.offset = 0.12,
ptm.pad = 0.35,
ptm.marker.size = marker.size/4.5,
clv.col = NULL,
clv.symbol = "triangle-down",
clv.offset = 0.12,
clv.pad = 0.35,
clv.marker.size = marker.size/4,
annotate.position.every = 10,
annotate.position.alpha = 0.5,
annotate.position.ay = -0.4 * marker.size,
position.font.size = font.size - 6,
legend.xy = c(0.97, 0.954),
legend.xanchor = "left",
legend.yanchor = "top",
legend.orientation = "v",
legend.col = NULL,
legend.bg = "#FFFFFF00",
legend.border.col = "#FFFFFF00",
legend.borderwidth = 0,
legend.group.gap = 0,
margin = list(b = 0, l = 0, t = 0, r = 0, pad = 0),
showgrid.x = FALSE,
showgrid.y = FALSE,
automargin.x = TRUE,
automargin.y = TRUE,
xaxis.autorange = TRUE,
yaxis.autorange = "reversed",
scaleanchor.y = "x",
scaleratio.y = 1,
hoverlabel.align = "left",
displayModeBar = TRUE,
modeBar.file.format = "svg",
scrollZoom = TRUE,
filename = NULL,
file.width = 1320,
file.height = 990,
file.scale = 1,
width = NULL,
height = NULL,
verbosity = 1,
...
)
x |
Character vector: amino acid sequence (1-letter abbreviations) OR
|
site |
Named list of lists with indices of sites. These will be highlighted by coloring the border of markers |
region |
Named list of lists with indices of regions. These will be
highlighted by coloring the markers and lines of regions using the
|
ptm |
List of post-translational modifications |
clv |
List of cleavage sites |
variant |
List of variant information |
disease.variants |
List of disease variant information |
n.per.row |
Integer: Number of amino acids to show per row |
main |
Character: Main title |
main.xy |
Numeric vector, length 2: x and y coordinates for title.
e.g. if |
main.xref |
Character: xref for title |
main.yref |
Character: yref for title |
main.xanchor |
Character: xanchor for title |
main.yanchor |
Character: yanchor for title |
layout |
Character: "1curve", "grid": type of layout to use |
show.markers |
Logical: If TRUE, show amino acid markers |
show.labels |
Logical: If TRUE, annotate amino acids with elements |
font.size |
Integer: Font size for labels |
label.col |
Color for labels |
scatter.mode |
Character: Mode for scatter plot |
marker.size |
Integer: Size of markers |
marker.col |
Color for markers |
marker.alpha |
Numeric: Alpha for markers |
marker.symbol |
Character: Symbol for markers |
line.col |
Color for lines |
line.alpha |
Numeric: Alpha for lines |
line.width |
Numeric: Width for lines |
show.full.names |
Logical: If TRUE, show full names of amino acids |
region.scatter.mode |
Character: Mode for scatter plot |
region.style |
Integer: Style for regions |
region.marker.size |
Integer: Size of region markers |
region.marker.alpha |
Numeric: Alpha for region markers |
region.marker.symbol |
Character: Symbol for region markers |
region.line.dash |
Character: Dash for region lines |
region.line.shape |
Character: Shape for region lines |
region.line.smoothing |
Numeric: Smoothing for region lines |
region.line.width |
Numeric: Width for region lines |
region.line.alpha |
Numeric: Alpha for region lines |
theme |
Character: Theme to use: Run |
region.palette |
Named list of colors for regions |
region.outline.only |
Logical: If TRUE, only show outline of regions |
region.outline.pad |
Numeric: Padding for region outline |
region.pad |
Numeric: Padding for region |
region.fill.alpha |
Numeric: Alpha for region fill |
region.fill.shape |
Character: Shape for region fill |
region.fill.smoothing |
Numeric: Smoothing for region fill |
bpadcx |
Numeric: Padding for region border |
bpadcy |
Numeric: Padding for region border |
site.marker.size |
Integer: Size of site markers |
site.marker.symbol |
Character: Symbol for site markers |
site.marker.alpha |
Numeric: Alpha for site markers |
site.border.width |
Numeric: Width for site borders |
site.palette |
Named list of colors for sites |
variant.col |
Color for variants |
disease.variant.col |
Color for disease variants |
showlegend.ptm |
Logical: If TRUE, show legend for PTMs |
ptm.col |
Named list of colors for PTMs |
ptm.symbol |
Character: Symbol for PTMs |
ptm.offset |
Numeric: Offset for PTMs |
ptm.pad |
Numeric: Padding for PTMs |
ptm.marker.size |
Integer: Size of PTM markers |
clv.col |
Color for cleavage site annotations |
clv.symbol |
Character: Symbol for cleavage site annotations |
clv.offset |
Numeric: Offset for cleavage site annotations |
clv.pad |
Numeric: Padding for cleavage site annotations |
clv.marker.size |
Integer: Size of cleavage site annotation markers |
annotate.position.every |
Integer: Annotate every nth position |
annotate.position.alpha |
Numeric: Alpha for position annotations |
annotate.position.ay |
Numeric: Y offset for position annotations |
position.font.size |
Integer: Font size for position annotations |
legend.xy |
Numeric vector, length 2: x and y coordinates for legend |
legend.xanchor |
Character: xanchor for legend |
legend.yanchor |
Character: yanchor for legend |
legend.orientation |
Character: Orientation for legend |
legend.col |
Color for legend |
legend.bg |
Color for legend background |
legend.border.col |
Color for legend border |
legend.borderwidth |
Numeric: Width for legend border |
legend.group.gap |
Numeric: Gap between legend groups |
margin |
List: Margin settings |
showgrid.x |
Logical: If TRUE, show x grid |
showgrid.y |
Logical: If TRUE, show y grid |
automargin.x |
Logical: If TRUE, use automatic margin for x axis |
automargin.y |
Logical: If TRUE, use automatic margin for y axis |
xaxis.autorange |
Logical: If TRUE, use automatic range for x axis |
yaxis.autorange |
Character: If TRUE, use automatic range for y axis |
scaleanchor.y |
Character: Scale anchor for y axis |
scaleratio.y |
Numeric: Scale ratio for y axis |
hoverlabel.align |
Character: Alignment for hover label |
displayModeBar |
Logical: If TRUE, display mode bar |
modeBar.file.format |
Character: File format for mode bar |
scrollZoom |
Logical: If TRUE, enable scroll zoom |
filename |
Character: File name to save plot |
file.width |
Integer: Width for saved file |
file.height |
Integer: Height for saved file |
file.scale |
Numeric: Scale for saved file |
width |
Integer: Width for plot |
height |
Integer: Height for plot |
verbosity |
Integer: If > 0, print messages to console. If > 1, print trace messages |
... |
Additional arguments to pass to the theme function |
A plotly object
E.D. Gennatas
## Not run:
tau <- seqinr::read.fasta("https://rest.uniprot.org/uniprotkb/P10636.fasta",
seqtype = "AA"
)
dplot3_protein(as.character(tau[[1]]))
# or directly using the UniProt accession number:
dplot3_protein("P10636")
## End(Not run)
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