plotNMFmeta: Plots coef results from NMF analysis

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

Plots coef results from NMF analysis

Description

Plots coef results from NMF analysis

Usage

plotNMFmeta(
  id,
  rank,
  label_scheme_sub,
  scale_log2r,
  complete_cases,
  impute_na,
  df,
  df2,
  filepath,
  filename,
  anal_type,
  ...
)

Arguments

id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
rank	Numeric vector; the factorization rank(s) in nmf. The default is c(4:8)
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.
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.
complete_cases	Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE.
impute_na	Logical; if TRUE, data with the imputation of missing values will be used. The default is TRUE.
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.
filepath	Use system default.
filename	A representative file name to outputs. By default, it will be determined automatically by the name of the current call.
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", ...).
...	filter_: Logical expression(s) for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements. arrange_: Variable argument statements for the row ordering against data in a primary file linked to df. See also prnHM for the format of arrange_ statements. Additional arguments for nmf.

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