massqc_sample_boxplot: massqc_sample_boxplot

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

massqc_sample_boxplot

Description

Boxplot for each samples.

Usage

massqc_sample_boxplot(
  object,
  color_by,
  fill_by,
  order_by = "sample_id",
  outlier.shape = NA,
  point = FALSE,
  point_alpha = 0.8
)

Arguments

object	tidymass-class object.
color_by	which column (sample_info) is used to color samples
fill_by	which column (sample_info) is used to fill samples
order_by	which column (sample_info) is used to order samples
outlier.shape	outlier.shape from ggplot2.
point	point or not.
point_alpha	point_alpha

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_sample_boxplot()

object %>%
  log(10) %>%
  massqc_sample_boxplot()

object %>%
  log(10) %>%
  massqc_sample_boxplot(color_by = "class")

object %>%
  log(10) %>%
  massqc_sample_boxplot(fill_by = "class") +
  ggsci::scale_fill_lancet()

object %>%
  log(10) %>%
  massqc_sample_boxplot(
    fill_by = "class",
    color_by = "class",
    point = TRUE,
    point_alpha = 0.3
  ) +
  ggsci::scale_fill_lancet()

object %>%
  log(10) %>%
  massqc_sample_boxplot(color_by = "class",
                 point = TRUE,
                 point_alpha = 0.3) +
  ggsci::scale_color_lancet()

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