Dotplot and Heatmap Generator
contact:jknight@lunenfeld.ca
User's Guide

Upload Data File  (Sample Input Files):
Input File (-f) File Format (-i)

Parameters:(default is suggested value)
Primary FDR cutoff (-s) Secondary FDR cutoff (-t)
Minimum spectral count (-x) Maximum spectral count (-m)
normalization (-N)

Clustering type:
clustering to perform (-c)

Clustering options:
distance metric (-d)
clustering type (-n)

   

Parameter descriptions
-f Input file name (Should be tab deliminated text format)
-i Input file format (SaintExpress or generic format. See sample input files for formatting examples.)
-s Primary FDR cutoff in range 0-1 (default 0.01)
-t Secondary FDR cutoff; must be higher than the primary (default 0.05)
-x Minimum spectral count for significant preys (default 0)
-m Maximum spectral count to visualize (default 50)
-N Normalization. Options: 0 for no normalization (default), 1 for yes based on total spectral counts, 2 for normalization based on significant preys counts (see option -C)
-C FDR cutoff for "significant" preys if normalization option 2 (-N 2) is used (default/recommended is the secondary FDR cutoff value -t)
-c Clustering to perform. Options: b (biclustering), h (hierarchical [default]), or n (none, requires input text files for bait and prey ordering; see options -b and -p)
-d Distance metric to use if option -c is set to "h". Options: binary, canberra (default), euclidean, manhattan, maximum or minkowski
-n Clustering type to be performed if option -c is set to "h". Options: average, centroid, complete, mcquitty, median, single, ward (default)
-b List of bait proteins in display order, one entry per line (only necessary if option -c is set to "n")
-p List of prey proteins in display order, one entry per line (only necessary if option -c is set to "n")
Source code