plot_pulldown: Create a scatterplot representing a pull-down
In dereksonderegger/PepSeq: Tools for analyzing Peptide Sequencing results

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 script reads the .csv file and creates a graph using ggplot2 and saves the graph to an output file. The function also invisibly returns the dataset used to create the graph.

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plot_pulldown(input, output_file = "pulldown.pdf", height = NULL,
  width = NULL, ymin = NULL, ymax = NULL, peaks = TRUE,
  peak_method = "PoT", peak_param = NA, scales = "free_y")

`input`	The input data frame read in using the 'import_pulldown()' function.
`output_file`	The file to save the resulting image. In can be a full path to the new file or a relative path from the current working directory.
`height`	The height (in inches) of the resulting file. If NULL, the default is the number of Group-by-Treatment-by-Rep combinations plus 3.
`width`	The width (in inches) of the resulting file. If NULL, the default is the number of sequences / 1000.
`ymin`	The minimum value of the response to be shown. If NULL, all the data is shown.
`ymax`	The maximum value of the response to be shown. If NULL, all the data is shown.
`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_y' across the rows or if the y-scales should be 'free_y' to vary across the different rows.

Critically this function assumes the .csv file has columns for 'protein_ID' and 'position' and that no other columns other than the read counts start with a 'X'.

dereksonderegger/PepSeq documentation built on July 24, 2019, 12:57 a.m.