dplot3_protein: Plot the primary amino acid sequence of a protein

In egenn/rtemis: Machine Learning and Visualization

Plot the primary amino acid sequence of a protein

Description

Plot the primary amino acid sequence of a protein

Usage

dplot3_protein(
  x,
  site = NULL,
  region = NULL,
  ptm = 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",
  marker.hoverinfo = "text",
  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 = 2:10,
  ptm.symbol = "circle",
  ptm.offset = 0.12,
  ptm.pad = 0.35,
  ptm.marker.size = marker.size/4.5,
  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,
  modebar.bg = "transparent",
  filename = NULL,
  file.width = 1320,
  file.height = 990,
  file.scale = 1,
  width = NULL,
  height = NULL,
  verbose = TRUE,
  trace = 0,
  ...
)

Arguments

x	Character vector of amino acid sequence (1-letter abbreviations)
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 palette colors
ptm	List of post-translational modifications
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 and main.yref are "paper": c(0.055, .975) is top left, c(.5, .975) is top and middle
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
marker.hoverinfo	Character: Hoverinfo 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 themes() for available themes
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
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
modebar.bg	Color for modebar background
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
verbose	Logical: If TRUE, print messages to console
trace	Integer: If > 0, print trace messages
...	Additional arguments to pass to the theme function

Value

A plotly object

Author(s)

E.D. Gennatas

Examples

## 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)

egenn/rtemis documentation built on May 4, 2024, 7:40 p.m.