feature_plot: Visualize feature (protein) variation among conditions

In promor: Proteomics Data Analysis and Modeling Tools

Visualize feature (protein) variation among conditions

Description

This function visualizes protein intensity differences among conditions (classes) using box plots or density distribution plots.

Usage

feature_plot(
  model_df,
  type = "box",
  text_size = 10,
  palette = "viridis",
  n_row,
  n_col,
  save = FALSE,
  file_path = NULL,
  file_name = "Feature_plot",
  file_type = "pdf",
  dpi = 80,
  plot_width = 7,
  plot_height = 7
)

Arguments

model_df	A model_df object from performing pre_process.
type	Type of plot to generate. Choices are "box" or "density." Default is "box."
text_size	Text size for plot labels, axis labels etc. Default is 10.
palette	Viridis color palette option for plots. Default is "viridis". See viridis for available options.
n_row	Number of rows to print the plots.
n_col	Number of columns to print the plots.
save	Logical. If TRUE saves a copy of the plot in the directory provided in file_path.
file_path	A string containing the directory path to save the file.
file_name	File name to save the plot. Default is "Feature_plot."
file_type	File type to save the plot. Default is "pdf".
dpi	Plot resolution. Default is 80.
plot_width	Width of the plot. Default is 7.
plot_height	Height of the plot. Default is 7.

Details

This function visualizes condition-wise differences in protein intensity using boxplots and/or density plots.

Value

A ggplot2 object

Author(s)

Chathurani Ranathunge

See Also

• pre_process, rem_feature

Examples

## Create a model_df object with default settings.
covid_model_df <- pre_process(covid_fit_df, covid_norm_df)

## Feature variation - box plots
feature_plot(covid_model_df, type = "box", n_row = 4, n_col = 2)

## Density plots
feature_plot(covid_model_df, type = "density")

## Change color palette
feature_plot(covid_model_df, type = "density", n_row = 4, n_col = 2, palette = "rocket")

promor documentation built on July 26, 2023, 5:39 p.m.