plot_pulldown_Shiny: Create a Shiny application showing a scatterplot representing...
In dereksonderegger/PepSeq: Tools for analyzing Peptide Sequencing results

Description Usage Arguments Details Examples

View source: R/Pulldown_Visualization_Shiny.R

The pulldown script created by John Altin creates a .csv file with several columns that gives the number of reads for various peptide sequences. This function reads the .csv file and creates a Shiny application that allows the user to explore the pulldown.

1 2	plot_pulldown_Shiny(input, height = 400, peaks = FALSE, peak_method = "PoT", peak_param = NA)

`input`	The input data frame read in using the 'import_pulldown()' function.
`height`	The height of the graph window (in pixels).
`peaks`	A logical flag denoting if the peaks should be highlighted
`peak_method`	Which method should be used for peak detection
`peak_param`	A parameter which controls the peak finding method. For PoT, it is the threshold.
`scales`	Contols if the y-scale should be 'fixed' across the rows or if the y-scales should be 'free' to vary across the different rows.

The input .csv file should have a columns denoting the protein name and location, (by default we assume they are labeled 'protein_ID' and 'position') and then a bunch of response columns. If the response column has a "XXX_cleaved" and "XXX_uncleaved" pair, then we standardize the cleaved/uncleaved pair into a single response. If the column has no pair, then we don't do any standardization with it.