Plot an amino acid sequence with annotations

Plot an amino acid sequence with multiple site and/or region annotations.

Usage

draw_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 = rtemis_theme,
  region_palette = rtemis_palette,
  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 = rtemis_palette,
  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 = 1L,
  ...
)

Arguments

x: Character vector: amino acid sequence (1-letter abbreviations) OR a3 object OR Character: path to JSON file OR Character: UniProt accession number.
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.
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 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.
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.
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: Verbosity level.
...: Additional arguments to pass to the theme function.

Value

A plotly object

Author

EDG

Examples

if (FALSE) { # \dontrun{
tau <- seqinr::read.fasta("https://rest.uniprot.org/uniprotkb/P10636.fasta",
  seqtype = "AA"
)
draw_protein(as.character(tau[[1]]))

# or directly using the UniProt accession number:
draw_protein("P10636")
} # }