plot_pulldown: Create a scatterplot representing a pull-down

Description Usage Arguments Details

View source: R/Pulldown_Visualization.R

Description

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.

Usage

1
2
3
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")

Arguments

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.

Details

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.