plotEucDist: Plots EucDist

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

Plots EucDist

Description

Plots EucDist

Usage

plotEucDist(
  df = NULL,
  id = NULL,
  label_scheme_sub = NULL,
  adjEucDist = FALSE,
  scale_log2r = TRUE,
  complete_cases = FALSE,
  annot_cols,
  annot_colnames,
  filepath = NULL,
  filename = NULL,
  anal_type = "EucDist",
  ...
)

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.
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.
adjEucDist	Logical; if TRUE, adjusts the inter-plex Euclidean distance by 1/sqrt(2) at method = "euclidean". The option adjEucDist = TRUE may be suitable when reference samples from each TMT plex undergo approximately the same sample handling process as the samples of interest. For instance, reference samples were split at the levels of protein lysates. Typically, adjEucDist = FALSE if reference samples were split near the end of a sample handling process, for instance, at the stages immediately before or after TMT labeling. Also see online README, section MDS for a brief reasoning.
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.
annot_cols	A character vector of column keys in expt_smry.xlsx. The values under the selected keys will be used to color-code sample IDs on the top of the indicated plot. The default is NULL without column annotation.
annot_colnames	A character vector of replacement name(s) to annot_cols. The default is NULL without name replacement.
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.
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_: 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. 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 parameters for plotting: width, the width of plot height, the height of plot Additional arguments for pheatmap: cluster_rows, clustering_method, clustering_distance_rows... Notes about pheatmap: annotation_col disabled; instead use keys indicated in annot_cols annotation_row disabled; instead use keys indicated in annot_rows

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