massqc_pca: massqc_pca

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

massqc_pca

Description

Boxplot for each samples.

Usage

massqc_pca(
  object,
  color_by,
  point_alpha = 0.8,
  frame = TRUE,
  frame.type = "norm",
  line = TRUE,
  ...
)

Arguments

object	tidymass-class object.
color_by	which column (sample_info) is used to color samples
point_alpha	point_alpha
frame	?ggplot2::autoplot
frame.type	?ggplot2::autoplot
line	Add lines or not.
...	other paramters for ggplot2::autoplot

Value

ggplot2 plot.

Author(s)

Xiaotao Shen [e-mail]

Examples

library(massdataset)
library(ggplot2)
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_pca()

object %>%
  massqc_pca(color_by = "class")

object %>%
  scale %>%
  massqc_pca(color_by = "class")

object %>%
  scale %>%
  massqc_pca(color_by = "class", frame = FALSE) +
  ggsci::scale_fill_lancet()

object %>%
  scale %>%
  massqc_pca(color_by = "class", frame = FALSE) +
  ggsci::scale_fill_lancet() +
  ggrepel::geom_text_repel(aes(label = sample_id))

object %>%
  scale %>%
  massqc_pca(color_by = "class", frame = FALSE) +
  ggsci::scale_fill_lancet() +
  ggrepel::geom_text_repel(aes(label = ifelse(class == "QC", sample_id, NA)))

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