show_sig_fit: Show Signature Fit Result

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Show Signature Fit Result

Description

See sig_fit for examples.

Usage

show_sig_fit(
  fit_result,
  samples = NULL,
  signatures = NULL,
  plot_fun = c("boxplot", "violin", "scatter"),
  palette = "aaas",
  title = NULL,
  xlab = FALSE,
  ylab = "Signature exposure",
  legend = "none",
  width = 0.3,
  outlier.shape = NA,
  add = "jitter",
  add.params = list(alpha = 0.3),
  ...
)

Arguments

fit_result	result object from sig_fit.
samples	samples to show, if NULL, all samples are used.
signatures	signatures to show.
plot_fun	set the plot function.
palette	the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
title	plot main title.
xlab	character vector specifying x axis labels. Use xlab = FALSE to hide xlab.
ylab	character vector specifying y axis labels. Use ylab = FALSE to hide ylab.
legend	character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); see details section.
width	numeric value between 0 and 1 specifying box width.
outlier.shape	point shape of outlier. Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.
add	character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.
add.params	parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").
...	other arguments to be passed to geom_boxplot, ggpar and facet.

Value

a ggplot object.

See Also

sig_fit, show_sig_bootstrap_exposure, sig_fit_bootstrap, sig_fit_bootstrap_batch

sigminer documentation built on May 29, 2024, 3:11 a.m.