gsVolcano: Volcano plots of protein 'log2FC' under given gene sets

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

Volcano plots of protein log2FC under given gene sets

Description

Volcano plots of protein log2FC under given gene sets

Usage

gsVolcano(
  df2 = NULL,
  df = NULL,
  contrast_groups = NULL,
  gsea_key = "term",
  gsets = NULL,
  theme = NULL,
  fml_nm = NULL,
  filepath = NULL,
  filename = NULL,
  adjP = FALSE,
  topn_labels = 20,
  show_sig = "none",
  gspval_cutoff = 1e-06,
  gslogFC_cutoff = log2(1.2),
  topn_gsets = Inf,
  ...
)

Arguments

df2	Character vector or string; the name(s) of secondary data file(s). An informatic task, i.e. anal_prnTrend(...) against a primary df generates secondary files such as Protein_Trend_Z_nclust6.txt etc. See also prnHist for the description of a primary df; normPSM for the lists of df and df2.
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").
contrast_groups	The contrast groups defined under a formula at fml_nm.
gsea_key	Character string; the column key indicating the terms of gene sets.
gsets	The gene sets.
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.
show_sig	Character string indicating the type of significance values to be shown with gspaMap. The default is "none". Additional choices are from c("pVal", "qVal") where pVal or qVal will be shown, respectively, in the facet grid of the plots.
gspval_cutoff	Numeric value or vector for uses with gspaMap. Gene sets with enrichment pVals less significant than the threshold will be excluded from volcano plot visualization. The default significance is 0.05 for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of cut-off values.
gslogFC_cutoff	Numeric value or vector for uses with gspaMap. Gene sets with absolute enrichment log2FC less than the threshold will be excluded from volcano plot visualization. The default magnitude is log2(1.2) for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of absolute values in log2FC.
topn_gsets	Numeric value or vector; top entries in gene sets ordered by increasing pVal for visualization. The default is to use all available entries. Note that it is users' responsibility to ensure that the custom gene sets contain terms that can be found from the one or multiple preceding analyses of prnGSPA. For simplicity, it is generally applicable to include all of the data bases that have been applied to prnGSPA and in that way no terms will be missed for visualization. See also prnGSPA for examples of custom data bases.
...	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 March 16, 2024, 5:27 a.m.