show_sig_fit function

Show Signature Fit Result

Show Signature Fit Result

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.

Returns

a ggplot object.

See Also

sig_fit , show_sig_bootstrap_exposure , sig_fit_bootstrap , sig_fit_bootstrap_batch