fullVolcano: Volcano plots for all proteins or peptides in a data set

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Volcano plots for all proteins or peptides in a data set

Description

Volcano plots for all proteins or peptides in a data set

Usage

fullVolcano(
  df = NULL,
  id = "gene",
  contrast_groups = NULL,
  theme = NULL,
  fml_nm = NULL,
  filepath = NULL,
  filename = NULL,
  adjP = FALSE,
  topn_labels = 20,
  highlights = NULL,
  grids = NULL,
  ...
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
contrast_groups	The contrast groups defined under a formula at fml_nm.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
fml_nm	A character string; the name of fml.
filepath	A file path to output results. By default, it will be determined automatically by the name of the calling function and the value of id in the call.
filename	A representative file name to outputs. By default, the name(s) will be determined automatically. For text files, a typical file extension is .txt. For image files, they are typically saved via ggsave or pheatmap where the image type will be determined by the extension of the file name.
adjP	Logical; if TRUE, use Benjamini-Hochberg pVals in volcano plots. The default is FALSE.
topn_labels	A non-negative integer; the top-n species for labeling in a plot. At topn_labels = 0, no labels of proteins/peptides will be shown. The default is to label the top-20 species with the lowest p-values.
highlights	A list of entries for highlighting. See also filter_ varargs for the format.
grids	An integer or integer vector for subset visualization of contrasts within a group. For example with a group of three contrasts, grids = 2:3 will hide the first grid from displaying. At the NULL default, all available grids will be shown.
...	filter_: Variable argument statements for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements. Additional parameters for plotting: xco, the cut-off lines of fold changes at position x; the default is at -1.2 and +1.2. yco, the cut-off line of pVal at position y; the default is 0.05. width, the width of plot; height, the height of plot. nrow, the number of rows in a plot. xmin, the minimum x. xmax, the maximum x. ymin, the minimum y. ymax, the maximum y. x_label, the label on x. y_label, the label on y.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.