draw_protein: Plot an amino acid sequence with annotations

In egenn/rtemis: Machine Learning and Visualization

Plot an amino acid sequence with annotations

Description

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 = choose_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	Theme object.
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.

Value

plotly object.

Author(s)

EDG

Examples

## Not run: 
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")

## End(Not run)

egenn/rtemis documentation built on June 14, 2025, 11:54 p.m.