Description Usage Arguments Details
View source: R/Pulldown_Visualization.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 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.
1 2 3 |
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'.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.