massqc_pca_pc1 — massqc_pca

Boxplot for each samples.

massqc_pca_pc1(
  object,
  color_by,
  order_by,
  point_alpha = 0.8,
  point_size = 3,
  desc = FALSE
)

Arguments

object: tidymass-class object.
color_by: which column (sample_info) is used to color samples
order_by: which column (sample_info) is used to order samples
point_alpha: point_alpha
point_size: point_size
desc: desc

Value

ggplot2 plot.

Author

Xiaotao Shen shenxt1990@163.com

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_pc1()
#> Warning: MVs in you object,
#>             
#> will remove variables > 50% and imputate with zero.


object %>%
  massqc_pca_pc1(color_by = "class")
#> Warning: MVs in you object,
#>             
#> will remove variables > 50% and imputate with zero.


object %>%
  scale %>%
  massqc_pca_pc1(color_by = "class")
#> Warning: MVs in you object,
#>             
#> will remove variables > 50% and imputate with zero.


object %>%
  scale %>%
  massqc_pca_pc1(
    color_by = "class",
    order_by = "injection.order",
    point_alpha = 1,
    point_size = 5
  ) +
  ggsci::scale_color_lancet()
#> Warning: MVs in you object,
#>             
#> will remove variables > 50% and imputate with zero.


object %>%
  scale %>%
  massqc_pca_pc1(
    color_by = "class",
    order_by = "injection.order",
    point_alpha = 1,
    point_size = 5,
    desc = TRUE
  ) +
  ggsci::scale_color_lancet()
#> Warning: MVs in you object,
#>             
#> will remove variables > 50% and imputate with zero.