algnmt_plot: Plot sequence alignments as ggplot object
In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

algnmt_plot

R Documentation

Plot sequence alignments as ggplot object

Description

Plot sequence alignments as ggplot object

Usage

algnmt_plot(
  algnmt,
  color_values = NULL,
  tile.border.color = NA,
  tile.border.on.NA = F,
  text = F,
  line = F,
  line_args = list(linewidth = 0.1, color = "black"),
  theme = ggplot2::theme_bw(),
  theme_args = list(panel.grid = ggplot2::element_blank()),
  pattern_lim_size = 0,
  pattern_lim_pos = "inner",
  pattern_names = F,
  pattern_names_fun = ggrepel::geom_text_repel,
  pairwiseAlignment = NULL,
  subject_lim_lines = F,
  subject_name = NULL,
  pos_col = "position",
  seq_col = "seq",
  name_col = "seq.name",
  start_end_col = "start_end",
  y_group_col = NULL,
  coord_fixed_ratio = NULL,
  x_breaks = NULL,
  algnmt_type = NULL,
  add_length_suffix = F,
  group_on_yaxis = F,
  min_gap = 10,
  ref = NULL,
  pos_shift = NULL,
  pos_shift_adjust_axis = T,
  verbose = T
)

Arguments

`algnmt`	an alignment object returned from (i) igsc::MultiplePairwiseAlignmentsToOneSubject, (ii) DECIPHER::AlignSeqs or (iii) Biostrings::pairwiseAlignment; in case (i) this is a data.frame, in case (ii) this is a XStringSet, in case (iii) this is a PairwiseAlignmentsSingleSubject; alternatively provide a custom data frame which has at least to contain pos_col, seq_col, name_col (see other arguments)
`color_values`	a color scale for NTs or AAs (depending on type of algnmt); provide a named vector of colors where names are NTs or AAs; or choose a name from igsc:::scheme_NT or igsc:::scheme_AA; or choose one from names(purrr::flatten(Peptides:::AAdata)); or leave NULL for the default scheme
`tile.border.color`	a color to draw tile borders with; e.g. "black" or a hex code; leave NA to have no borders (quicker plotting and advised for long alignments)
`tile.border.on.NA`	logical whether to draw borders on NA positions
`text`	logical whether to draw text in tiles (NT or AA identifier); or numeric indicating text size for geom_text() advisable only for short alignments
`theme`	ggplot theme to use as basis
`pattern_lim_size`	numeric; plot annotation of pattern alignment limits; value indicates size; set to 0 to omit plotting; only applicable if pa is provided
`subject_lim_lines`	logical whether to plot vertical lines of subject alignment limits
`subject_name`	name of the subject sequence in algnmt; only needed if subject_lim_lines = TRUE
`pos_col`	name of position column in algnmt (applicable if algnmt is a data.frame)
`seq_col`	name of sequence column in algnmt (applicable if algnmt is a data.frame)
`name_col`	name of column which holds sequence names in algnmt (applicable if algnmt is a data.frame)
`coord_fixed_ratio`	numeric; fixed aspect ratio of plot; leave NULL to not force a ratio
`x_breaks`	numeric vector; manually provide breaks (ticks) on x-axis; set NULL to have breaks picked automatically
`algnmt_type`	'NT' or 'AA'; only required if algnmt is a data.frame and only if NT or AA cannot be guessed; leave NULL to have it guessed based on data
`ref`	a reference sequence to compare all other sequnces to; e.g. a consensus sequence
`verbose`	made with DECIPHER::ConsensusSequence; if provided matching residues are replaced by a dot (.)