massqc_sample_correlation: massqc_sample_correlation

In tidymass/massqc: Quality assessment of LC-MS based metabolomics data

massqc_sample_correlation

Description

Boxplot for each samples.

Usage

massqc_sample_correlation(
  object,
  cor_method = c("spearman", "kendall", "pearson"),
  method = c("circle", "square"),
  type = c("full", "lower", "upper"),
  ggtheme = ggplot2::theme_bw,
  title = "",
  show.legend = TRUE,
  legend.title = "Correlation",
  show.diag = FALSE,
  colors = c("blue", "white", "red"),
  outline.color = "gray",
  hc.order = FALSE,
  order_by,
  hc.method = "complete",
  lab = FALSE,
  lab_col = "black",
  lab_size = 4,
  p.mat = NULL,
  sig.level = 0.05,
  insig = c("pch", "blank"),
  pch = 4,
  pch.col = "black",
  pch.cex = 5,
  tl.cex = 12,
  tl.col = "black",
  tl.srt = 45,
  digits = 2
)

Arguments

object	tidymass-class object.
cor_method	?cor
method	?ggcorrplot
type	?ggcorrplot
ggtheme	?ggcorrplot
title	?ggcorrplot
show.legend	?ggcorrplot
legend.title	?ggcorrplot
show.diag	?ggcorrplot
colors	?ggcorrplot
outline.color	?ggcorrplot
hc.order	?ggcorrplot
order_by	?ggcorrplot
hc.method	?ggcorrplot
lab	?ggcorrplot
lab_col	?ggcorrplot
lab_size	?ggcorrplot
p.mat	?ggcorrplot
sig.level	?ggcorrplot
insig	?ggcorrplot
pch	?ggcorrplot
pch.col	?ggcorrplot
pch.cex	?ggcorrplot
tl.cex	?ggcorrplot
tl.col	?ggcorrplot
tl.srt	?ggcorrplot
digits	?ggcorrplot

Value

ggplot2 plot.

Author(s)

Xiaotao Shen [e-mail]

Examples

library(massdataset)
data("expression_data")
data("sample_info")
data("variable_info")

object =
  create_mass_dataset(
    expression_data = expression_data,
    sample_info = sample_info,
    variable_info = variable_info
  )

object %>%
  massqc_sample_correlation()

object %>%
  massqc_sample_correlation()

object %>%
  activate_mass_dataset(what = "sample_info") %>%
  filter(class == "QC") %>%
  massqc_sample_correlation()

object %>%
  massqc_sample_correlation(lab = TRUE)

object %>%
  massqc_sample_correlation(lab = TRUE, type = "upper")

tidymass/massqc documentation built on Sept. 13, 2023, 10:31 p.m.