plotCorr: Correlation plots

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

Correlation plots

Description

Correlation plots

Usage

plotCorr(
  df = NULL,
  id = NULL,
  anal_type,
  data_select,
  col_select = NULL,
  col_order = NULL,
  label_scheme_sub = NULL,
  scale_log2r = TRUE,
  complete_cases = FALSE,
  filepath = NULL,
  filename = NULL,
  cor_method = "pearson",
  digits = 2L,
  ...
)

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.
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", ...).
data_select	The type of data to be selected, for example, logFC or logInt.
col_select	Character string to a column key in expt_smry.xlsx. At the NULL default, the column key of Select in expt_smry.xlsx will be used. In the case of no samples being specified under Select, the column key of Sample_ID will be used. The non-empty entries under the ascribing column will be used in indicated analysis.
col_order	Character string to a column key in expt_smry.xlsx. Numeric values under which will be used for the left-to-right arrangement of samples in graphic outputs or top-to-bottom arrangement in text outputs. At the NULL default, the column key Order will be used. If values under column Order are left blank, samples will be ordered by their names.
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.
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.
cor_method	A character string indicating which correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman".
digits	The number of decimal places in correlation values to be displayed.
...	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: width, the width of plot height, the height of plot xmin, the minimum x of logFC or intensity xmax, the maximum x of logFC data or intensity data xbreaks, the breaks on x axis; the same breaks will be applied to y axis.

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