volcano_plot: volcano_plot

In jaspershen/massstat: Statistical analysis for LC-MS-based metabolomics data

volcano_plot

Description

Draw volcano plot.

Usage

volcano_plot(
  object,
  fc_column_name = "fc",
  p_value_column_name = "p_value_adjust",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-adjust, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  line_color = "red",
  up_color = "#EE0000FF",
  down_color = "#3B4992FF",
  no_color = "#808180FF",
  point_size = 2,
  point_alpha = 1,
  point_size_scale,
  line_type = 1,
  add_text = FALSE,
  text_for = c("marker", "UP", "DOWM"),
  text_from = "variable_id"
)

Arguments

object	tidymass-class object.
fc_column_name	fc_column_name
p_value_column_name	p_value_column_name
labs_x	labs_x
labs_y	labs_y
fc_up_cutoff	fc_up_cutoff
fc_down_cutoff	fc_down_cutoff
p_value_cutoff	p_value_cutoff
line_color	line_color
up_color	up_color
down_color	down_color
no_color	no_color
point_size	point_size
point_alpha	point_alpha
point_size_scale	point_size_scale
line_type	line_type
add_text	add_text
text_for	text_for
text_from	text_from

Value

ggplot2 object

Author(s)

Xiaotao Shen [e-mail]

Examples

library(massdataset)
library(magrittr)
library(dplyr)

data("liver_aging_pos")
liver_aging_pos

w_78 =
  liver_aging_pos %>%
  activate_mass_dataset(what = "sample_info") %>%
  dplyr::filter(group == "78W") %>%
  dplyr::pull(sample_id)

w_24 =
  liver_aging_pos %>%
  activate_mass_dataset(what = "sample_info") %>%
  dplyr::filter(group == "24W") %>%
  dplyr::pull(sample_id)

control_sample_id = w_24
case_sample_id = w_78

liver_aging_pos =
  mutate_fc(
    object = liver_aging_pos,
    control_sample_id = control_sample_id,
    case_sample_id = case_sample_id,
    mean_median = "mean"
  )

liver_aging_pos =
  mutate_p_value(
    object = liver_aging_pos,
    control_sample_id = control_sample_id,
    case_sample_id = case_sample_id,
    method = "t.test",
    p_adjust_methods = "BH"
  )

object = liver_aging_pos

volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value_adjust",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-adjust, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = TRUE
)


volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-value, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = FALSE,
  point_alpha = 0.5
)

volcano_plot(
  object = object,
  fc_column_name = "fc",
  p_value_column_name = "p_value",
  labs_x = "log2(Fold change)",
  labs_y = "-log(p-value, 10)",
  fc_up_cutoff = 2,
  fc_down_cutoff = 0.5,
  p_value_cutoff = 0.05,
  add_text = FALSE,
  point_alpha = 0.5,
  point_size_scale = "p_value"
) +
  scale_size_continuous(range = c(0.5, 3))

jaspershen/massstat documentation built on Sept. 29, 2022, 4:30 a.m.