ggplot_mass_dataset: Create ggplot2 Visualization for a mass_dataset Object

In tidymass/massdataset: massdataset

Create ggplot2 Visualization for a mass_dataset Object

Description

This function generates a ggplot2 visualization for a mass_dataset object. You can choose the direction of the visualization (either "variable" or "sample"), specify the variable or sample of interest, and create various plots based on the chosen direction and data.

Usage

ggplot_mass_dataset(
  object,
  direction = c("variable", "sample"),
  variable_index = 1,
  variable_id,
  sample_index = 1,
  sample_id
)

Arguments

object	A mass_dataset object.
direction	A character vector specifying the direction of the visualization. It can be either "variable" or "sample". Default is "variable".
variable_index	An integer specifying the index of the variable of interest. If not provided, you can use 'variable_id' to specify the variable by its ID.
variable_id	A character string specifying the ID of the variable of interest. If provided, 'variable_index' will be ignored.
sample_index	An integer specifying the index of the sample of interest. If not provided, you can use 'sample_id' to specify the sample by its ID.
sample_id	A character string specifying the ID of the sample of interest. If provided, 'sample_index' will be ignored.

Value

A ggplot2 plot object.

Author(s)

Xiaotao Shen [e-mail]

Examples

data("expression_data")
data("sample_info")
data("variable_info")
object =
  create_mass_dataset(
    expression_data = expression_data,
    variable_info = variable_info,
    sample_info = sample_info
  )
library(ggplot2)
ggplot_mass_dataset(object, direction = "variable", 
                    variable_index = 1) +
  geom_boxplot(aes(x = class, color = class)) +
  geom_jitter(aes(x = class, color = class))

object %>% 
  `+`(1) %>% 
  log(10) %>% 
  scale() %>% 
ggplot_mass_dataset(direction = "sample", 
                    sample_index = 2) +
  geom_boxplot(aes(x = 1)) +
  geom_jitter(aes(x = 1, color = mz))

tidymass/massdataset documentation built on Jan. 30, 2024, 2:55 p.m.