See sig_fit for examples.

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