- Changes only to the Rscript make_logo_report.R (and README files) to indicate to use ggseqlogoMOD instead of ggseqlogo following a rename of this forked package.
- Changes in this Rscript also increased the font size of the axes of the logo plots, and corrected a ggplot2 parameter name, removing some related deprecation warning message.
- Added optional arguments
MHC2,no_bestPepResp,kmer,alphabet,unk_aa,col_scheme,theta_norm,flat_freq,Salign(see the README for details about these options). - The number of peptides below each motif in the report now corresponds to number of peptides assigned to this motif, after assigning each peptide to one motif based on its highest responsibility value (instead of considering fractional values based on the peptides's weight and responsibilities).
- The flat motif now has the same length as the other motifs (it does not show anymore the values used for this flat motif in the deconvolution as it was confusing to see motifs of different sizes).
- Updated license-related contact person.
- Improved the layout of the html report, of the readme and other small changes.
- Public release of MoDec version 1.0.