Visualize feature (protein) variation among conditions

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.

Value

A ggplot2 object

Details

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

Author

Chathurani Ranathunge

Examples


## Create a model_df object with default settings.
covid_model_df <- pre_process(covid_fit_df, covid_norm_df)
#> Total number of differentially expressed proteins (8) is less than n_top.
#> None of the proteins show high pair-wise correlation.
#> 
#> No highly correlated proteins to be removed.

## Feature variation - box plots
feature_plot(covid_model_df, type = "box", n_row = 4, n_col = 2)
#> Using condition as id variables


## Density plots
feature_plot(covid_model_df, type = "density")
#> Using condition as id variables


## Change color palette
feature_plot(covid_model_df, type = "density", n_row = 4, n_col = 2, palette = "rocket")
#> Using condition as id variables