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),
...
)result object from sig_fit.
samples to show, if NULL, all samples are used.
signatures to show.
set the plot function.
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".
plot main title.
character vector specifying x axis labels. Use xlab = FALSE to hide xlab.
character vector specifying y axis labels. Use ylab = FALSE to hide ylab.
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.
numeric value between 0 and 1 specifying box width.
Default aesthetics for outliers. Set to NULL to inherit from the
aesthetics used for the box.
In the unlikely event you specify both US and UK spellings of colour, the US spelling will take precedence.
Sometimes it can be useful to hide the outliers, for example when overlaying
the raw data points on top of the boxplot. Hiding the outliers can be achieved
by setting outlier.shape = NA. Importantly, this does not remove the outliers,
it only hides them, so the range calculated for the y-axis will be the
same with outliers shown and outliers hidden.
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_mad", "median_range"; see ?desc_statby for more details.
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.
a ggplot object.
sig_fit, show_sig_bootstrap_exposure, sig_fit_bootstrap, sig_fit_bootstrap_batch