hpgltools: A pile of (hopefully) useful R functions

combine_extracted_plots

R Documentation

Gather data required to make MA/Volcano plots for pairwise comparisons.

Description

It should be possible to significantly simplify the arguments passed to this function, but I have thus far focused only on getting it to work with the newly split-apart combine_de_tables() functions.

Usage

combine_extracted_plots(
  name,
  combined,
  denominator,
  numerator,
  plot_inputs,
  plot_basic = TRUE,
  plot_deseq = TRUE,
  plot_edger = TRUE,
  plot_limma = TRUE,
  plot_ebseq = FALSE,
  plot_noiseq = FALSE,
  loess = FALSE,
  logfc = 1,
  pval = 0.05,
  found_table = NULL,
  p_type = "all",
  plot_colors = NULL,
  fancy = FALSE,
  adjp = TRUE,
  do_inverse = FALSE,
  invert_colors = FALSE,
  z = 1.5,
  alpha = 0.4,
  z_lines = FALSE,
  label = 10,
  label_column = "hgncsymbol"
)

Arguments

`name`	Name of the table to plot.
`combined`	Modified pairwise result, containing the various DE methods.
`denominator`	Name of the denominator coefficient.
`numerator`	Name of the numerator coefficient.
`plot_inputs`	The individual outputs from limma etc.
`plot_basic`	Add basic data?
`plot_deseq`	Add deseq data?
`plot_edger`	Add edger data?
`plot_limma`	Add limma data?
`plot_ebseq`	Add ebseq data?
`plot_noiseq`	Add noiseq plots?
`loess`	Add a loess estimation?
`logfc`	For Volcano/MA plot lines.
`pval`	For Volcano/MA plot lines.
`found_table`	The table name actually used.
`p_type`	Use this/these methods' p-value for determining significance.
`plot_colors`	Use these colors for numerators/denominators.
`fancy`	Include fancy pdf/svg versions of plots for publication?
`adjp`	Use adjusted p-values?
`do_inverse`	Flip the numerator/denominator?
`invert_colors`	Conversely, keep the values the same, but flip the colors. I think these invert parameters are not needed anymore.
`z`	Use a z-score cutoff for coefficient plots.
`alpha`	Add some transparency to the plots.
`z_lines`	Add lines for zscore cutoffs?
`label`	Label this number of the top genes.
`label_column`	Label the top genes with this column.