byfile_plotVolcano: Plot volcanos

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

Plot volcanos

Description

Plot volcanos

Usage

byfile_plotVolcano(
  df = NULL,
  df2 = NULL,
  id = "gene",
  fml_nm = NULL,
  filepath = NULL,
  filename = NULL,
  adjP = FALSE,
  topn_labels = 20,
  anal_type = "Volcano",
  gset_nms = "go_sets",
  scale_log2r = TRUE,
  impute_na = FALSE,
  theme = 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").
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.
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
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.
anal_type	Character string; the type of analysis that are preset for method dispatch in function factories. The value will be determined automatically. Exemplary values include anal_type = c("PCA", "Corrplot", "EucDist", "GSPA", "Heatmap", "Histogram", "MDS", "Model", "NMF", "Purge", "Trend", "LDA", ...).
gset_nms	Character string or vector containing the shorthanded name(s), full file path(s), or both, to gene sets for enrichment analysis. For species among "human", "mouse", "rat", the default of c("go_sets", "c2_msig", "kinsub") will utilize terms from gene ontology (GO), molecular signatures (MSig) and kinase-substrate network (PSP Kinase-Substrate). Custom GO, MSig and other data bases at given species are also supported. See also: prepGO for the preparation of custom GO; prepMSig for the preparation of custom MSig. For other custom data bases, follow the same format of list as GO or MSig.
scale_log2r	Logical; if TRUE, adjusts log2FC to the same scale of standard deviation across all samples. The default is TRUE. At scale_log2r = NA, the raw log2FC without normalization will be used.
impute_na	Logical; if TRUE, data with the imputation of missing values will be used. The default is FALSE.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
...	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.