plot_intensities_ratio {metaprotr} | R Documentation |
plot_intensities_ratio
Description
Generates a scatter plot of the log2 (ratio + 1) between two conditions considering the spectral counts of each entity (peptides, subgroups, groups or taxonomic levels) from a "spectral_count_object". If a given condition has several replicates the mean value is taken into account.
Usage
plot_intensities_ratio(
spectral_count_object,
target_variable,
list_conditions,
force = FALSE
)
Arguments
spectral_count_object |
List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts organized by peptides, subgroups, groups or taxonomic levels. The format of this object is similar to that generated from the functions "getsc_specific" and "crumble_taxonomy". |
target_variable |
Character indicating the variable name containing the conditions to be compared. This value corresponds to the name of one column from metadata. |
list_conditions |
Atomic vector indicating two conditions to A be compared. The first element is considered as the reference (denominator) for ratio calculations. |
force |
Logic value set at FALSE by default in order to ask permission to create object in the workstation of the user. |
Value
A scatter plot (pdf) indicating the log2 (ratio + 1) of the entities (peptides, soubgroups, groups, taxonomic) between the two conditions provided.
Examples
data(fecal_waters)
plot_intensities_ratio(fecal_waters, "Methods", c("EF", "S"))
plot_intensities_ratio(fecal_waters, "SC_name", c("Q1", "Q2"))