byfile_plotVolcano.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/volcanos.R
\name{byfile_plotVolcano}
\alias{byfile_plotVolcano}
\title{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{
\item{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
\code{id} among \code{c("pep_seq", "pep_seq_mod", "prot_acc", "gene")}. A
primary file contains normalized peptide or protein data and is among
\code{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 \code{df} will be one of
\code{c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt",
"protein_impNA_pVal.txt")}.}

\item{df2}{Character vector or string; the name(s) of secondary data file(s).
An informatic task, i.e. \code{anal_prnTrend(...)} against a primary
\code{df} generates secondary files such as
\code{Protein_Trend_Z_nclust6.txt} etc. See also \code{\link{prnHist}} for
the description of a primary \code{df}; \code{\link{normPSM}} for the lists
of \code{df} and \code{df2}.}

\item{id}{Character string; one of \code{pep_seq}, \code{pep_seq_mod},
\code{prot_acc} and \code{gene}.}

\item{fml_nm}{A character string; the name of \code{fml}.}

\item{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 \code{id} in the \code{call}.}

\item{filename}{A representative file name to outputs. By default, the
name(s) will be determined automatically. For text files, a typical file
extension is \code{.txt}. For image files, they are typically saved via
\code{\link[ggplot2]{ggsave}} or \code{\link[pheatmap]{pheatmap}} where the
image type will be determined by the extension of the file name.}

\item{adjP}{Logical; if TRUE, use Benjamini-Hochberg pVals in volcano plots.
The default is FALSE.}

\item{topn_labels}{A non-negative integer; the top-n species for labeling in a
plot. At \code{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.}

\item{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 \code{anal_type = c("PCA",
"Corrplot", "EucDist", "GSPA", "Heatmap", "Histogram", "MDS", "Model",
"NMF", "Purge", "Trend", "LDA", ...)}.}

\item{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 \code{"human", "mouse", "rat"}, the default of
\code{c("go_sets", "c2_msig", "kinsub")} will utilize terms from gene
ontology (\code{GO}), molecular signatures (\code{MSig}) and
kinase-substrate network (\code{PSP Kinase-Substrate}). Custom \code{GO},
\code{MSig} and other data bases at given species are also supported. See
also: \code{\link{prepGO}} for the preparation of custom \code{GO};
\code{\link{prepMSig}} for the preparation of custom \code{MSig}. For other
custom data bases, follow the same format of list as \code{GO} or
\code{MSig}.}

\item{scale_log2r}{Logical; if TRUE, adjusts \code{log2FC} to the same scale
of standard deviation across all samples. The default is TRUE. At
\code{scale_log2r = NA}, the raw \code{log2FC} without normalization will
be used.}

\item{impute_na}{Logical; if TRUE, data with the imputation of missing values
will be used. The default is FALSE.}

\item{theme}{A
\href{https://ggplot2.tidyverse.org/reference/ggtheme.html}{ggplot2} theme,
i.e., theme_bw(), or a custom theme. At the NULL default, a system theme
will be applied.}

\item{...}{\code{filter_}: Variable argument statements for the row filtration
against data in a primary file linked to \code{df}. See also
\code{\link{normPSM}} for the format of \code{filter_} statements. \cr \cr
Additional parameters for plotting: \cr \code{xco}, the cut-off lines of
fold changes at position \code{x}; the default is at \eqn{-1.2} and
\eqn{+1.2}. \cr \code{yco}, the cut-off line of \code{pVal} at position
\code{y}; the default is \eqn{0.05}. \cr \code{width}, the width of plot;
\cr \code{height}, the height of plot. \cr \code{nrow}, the number of rows
in a plot. \cr \code{xmin}, the minimum \code{x}. \cr \code{xmax}, the
maximum \code{x}. \cr \code{ymin}, the minimum \code{y}. \cr \code{ymax},
the maximum \code{y}. \cr \code{x_label}, the label on \code{x}. \cr
\code{y_label}, the label on \code{y}.}
}
\description{
Plot volcanos
}