sigminer (version 1.2.5)

show_sig_profile: Show Signature Profile

Description

Who don't like to show a barplot for signature profile? This is for it.

Usage

show_sig_profile(
  Signature,
  mode = c("SBS", "copynumber", "DBS", "ID", "RS"),
  method = "Wang",
  by_context = FALSE,
  normalize = c("row", "column", "raw", "feature"),
  y_tr = NULL,
  filters = NULL,
  feature_setting = sigminer::CN.features,
  style = c("default", "cosmic"),
  palette = use_color_style(style, ifelse(by_context, "SBS", mode), method),
  set_gradient_color = FALSE,
  free_space = "free_x",
  rm_panel_border = style == "cosmic",
  rm_grid_line = style == "cosmic",
  rm_axis_text = FALSE,
  bar_border_color = ifelse(style == "default", "grey50", "white"),
  bar_width = 0.7,
  paint_axis_text = TRUE,
  x_label_angle = ifelse(mode == "copynumber" & !(startsWith(method, "T") | method ==
    "X"), 60, 90),
  x_label_vjust = ifelse(mode == "copynumber" & !(startsWith(method, "T") | method ==
    "X"), 1, 0.5),
  x_label_hjust = 1,
  x_lab = "Components",
  y_lab = "auto",
  params = NULL,
  show_cv = FALSE,
  params_label_size = 3,
  params_label_angle = 60,
  y_expand = 1,
  digits = 2,
  base_size = 12,
  font_scale = 1,
  sig_names = NULL,
  sig_orders = NULL,
  check_sig_names = TRUE
)

Arguments

Signature

a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix with row representing components (motifs) and column representing signatures (column names must start with 'Sig').

mode

signature type for plotting, now supports 'copynumber', 'SBS', 'DBS', 'ID' and 'RS' (genome rearrangement signature).

method

method for copy number feature classification in sig_tally, can be one of "Macintyre" ("M"), "Wang" ("W").

by_context

for specific use.

normalize

one of 'row', 'column', 'raw' and "feature", for row normalization (signature), column normalization (component), raw data, row normalization by feature, respectively. Of note, 'feature' only works when the mode is 'copynumber'.

y_tr

a function (e.g. log10) to transform y axis before plotting.

filters

a pattern used to select components to plot.

feature_setting

a data.frame used for classification. Only used when method is "Wang" ("W"). Default is CN.features. Users can also set custom input with "feature", "min" and "max" columns available. Valid features can be printed by unique(CN.features$feature).

style

plot style, one of 'default' and 'cosmic', works when parameter set_gradient_color is FALSE.

palette

palette used to plot when set_gradient_color is FALSE, default use a built-in palette according to parameter style.

set_gradient_color

default is FALSE, if TRUE, use gradient colors to fill bars. This is very useful when signatures are extracted from "Macintyre" method and normalize is 'column'.

free_space

default is 'free_x'. If "fixed", all panels have the same size. If "free_y" their height will be proportional to the length of the y scale; if "free_x" their width will be proportional to the length of the x scale; or if "free" both height and width will vary. This setting has no effect unless the appropriate scales also vary.

rm_panel_border

default is TRUE for style 'cosmic', remove panel border to keep plot tight.

rm_grid_line

default is FALSE, if TRUE, remove grid lines of plot.

rm_axis_text

default is FALSE, if TRUE, remove component texts. This is useful when multiple signature profiles are plotted together.

bar_border_color

the color of bar border.

bar_width

bar width. By default, set to 70% of the resolution of the data.

paint_axis_text

if TRUE, color on text of x axis.

x_label_angle

font angle for x label.

x_label_vjust

font vjust for x label.

x_label_hjust

font hjust for x label.

x_lab

x axis lab.

y_lab

y axis lab.

params

params data.frame of components, obtained from sig_tally.

show_cv

default is FALSE, if TRUE, show coefficient of variation when params is not NULL.

params_label_size

font size for params label.

params_label_angle

font angle for params label.

y_expand

y expand height for plotting params of copy number signatures.

digits

digits for plotting params of copy number signatures.

base_size

overall font size.

font_scale

a number used to set font scale.

sig_names

subset signatures or set name of signatures, can be a character vector. Default is NULL, prefix 'Sig' plus number is used.

sig_orders

set order of signatures, can be a character vector. Default is NULL, the signatures are ordered by alphabetical order. If an integer vector set, only specified signatures are plotted.

check_sig_names

if TRUE, check signature names when input is a matrix, i.e., all signatures (colnames) must start with 'Sig'.

Value

a ggplot object

See Also

show_sig_profile_loop, show_sig_profile_heatmap

Examples

# NOT RUN {
# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature profile
p1 <- show_sig_profile(sig2, mode = "SBS")
p1

# Use 'y_tr' option to transform values in y axis
p11 <- show_sig_profile(sig2, mode = "SBS", y_tr = function(x) x * 100)
p11

# Load copy number signature from method "W"
load(system.file("extdata", "toy_copynumber_signature_by_W.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature profile
p2 <- show_sig_profile(sig,
  style = "cosmic",
  mode = "copynumber",
  method = "W",
  normalize = "feature"
)
p2

# Load copy number signature from method "M"
load(system.file("extdata", "toy_copynumber_signature_by_M.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature profile
# The 'column' normalization is consistent with
# original paper
p3 <- show_sig_profile(sig,
  paint_axis_text = FALSE,
  mode = "copynumber",
  method = "M", normalize = "column"
)
p3

# Add params label
# =================
# Load copy number prepare object
load(system.file("extdata", "toy_copynumber_tally_M.RData",
  package = "sigminer", mustWork = TRUE
))
params <- get_tidy_parameter(cn_tally_M$components)
p4 <- show_sig_profile(sig,
  mode = "copynumber",
  method = "M", normalize = "column",
  params = params, y_expand = 2
)
p4

# Visualize rearrangement signatures
s <- get_sig_db("RS_Nik_lab")
ss <- s$db[, 1:3]
colnames(ss) <- c("Sig1", "Sig2", "Sig3")
p5 <- show_sig_profile(ss, mode = "RS", style = "cosmic")
p5
# }