Wood's plot
Creates a Wood's plot that plots log2 fold change of peptides or precursors along the protein sequence.
woods_plot( data, fold_change, start_position, end_position, protein_length, coverage = NULL, protein_id = NULL, facet = NULL, colouring = NULL, fold_change_cutoff = 1 )
data |
Data frame containing differential abundance, start and end peptide or precursor positions, protein length and optionally a variable based on which peptides or precursors should be coloured. |
fold_change |
Column in the data frame containing log2 fold changes. |
start_position |
Column in the data frame containing the start positions for each peptide or precursor. |
end_position |
Column in the data frame containing the end positions for each peptide or precursor. |
protein_length |
Column in the data frame containing the length of the protein. |
coverage |
Optional, column in the data frame containing coverage in percent. Will appear in the title of the barcode if provided. |
protein_id |
Optional argument, column in the data frame containing protein identifiers. Required if only one protein should be plotted and the data frame contains only information for this protein. |
facet |
Optional argument, column in the data frame containing information by which data should be faceted. This can be protein identifiers. |
colouring |
Optional argument, column in the data frame containing information by which peptide or precursors should be coloured. |
fold_change_cutoff |
Optional argument specifying the log2 fold change cutoff used for assessing whether changes are significant. The default value is 2. |
A Wood's plot is returned. Plotting peptide or precursor fold changes accross protein sequence.
## Not run: woods_plot(test, fold_change = diff, start_position = start, end_position = end, protein_length = length, colouring = pep_type, facet = pg_protein_accessions ) ## End(Not run)
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