This method creates a scatter plot of the log2 fold change for each metabolite.
Usage
plot_scatter(
log2fc_df,
show_labels_for = NULL,
values_col_name = "log2FC",
stat_col_name = "qval",
show_p_value = TRUE,
signif_colors = c(`#5F5F5F` = 1, `#FEBF6E` = 0.1, `#EE5C42` = 0.05, `#8B1A1A` = 0.01),
save_as = NULL,
folder_name = format(Sys.Date(), "%Y-%m-%d"),
folder_path = NULL,
file_name = "network",
format = "pdf",
width = 29.7,
height = 21,
units = "cm",
overwrite = FALSE
)Arguments
- log2fc_df
DF with metabolites as row names and columns including log2FC, Class, qval columns.
- show_labels_for
Vector with Strings of Metabolite names or classes.
- values_col_name
Column name of a column that holds numeric values, to be plotted Default = "log2FC"
- stat_col_name
Columnname that holds numeric stat values that are used for significance Default = "qval"
- show_p_value
Boolean Value, to color p-values according to their significance level and add a Legend Default = TRUE
- signif_colors
Vector assigning significance values different colors
- save_as
Optional: Select the file type of output plots. Options are svg, pdf, png or NULL. Default = "NULL"
- folder_name
Name of the folder where the plot will be saved. Special characters will be removed automatically. Default = date
- folder_path
Optional: User-defined path where the folder should be created. If not provided, results will be saved in `MetAlyzer_results` within the working directory. Default = NULL
- file_name
Name of the output file (without extension). Default = "network"
- format
File format for saving the plot (e.g., "png", "pdf", "svg"). Default = "pdf"
- width
Width of the saved plot in specified units. Default = 29.7
- height
Height of the saved plot in specified units. Default = 21.0
- units
Units for width and height (e.g., "in", "cm", "mm"). Default = "cm"
- overwrite
Logical: If `TRUE`, overwrite existing files without asking. If `FALSE`, prompt user before overwriting. Default = FALSE
Examples
log2fc_df <- readRDS(MetAlyzer::toy_diffres())
scatter <- MetAlyzer::plot_scatter(log2fc_df)