diff --git a/pmultiqc/modules/quantms/quantms.py b/pmultiqc/modules/quantms/quantms.py index 1406386..65ed425 100755 --- a/pmultiqc/modules/quantms/quantms.py +++ b/pmultiqc/modules/quantms/quantms.py @@ -938,26 +938,29 @@ def draw_search_engine(self): hyper_bar_html = bargraph.plot(list(self.search_engine['hyper'].values()), hyper_cats, hyper_pconfig) if self.Sage_label else '' - self.add_section( - description='''#### SpecEvalue Description - * SpecEvalue : Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue). - ''', - plot= SpecE_bar_html - ) + if SpecE_bar_html != '': + self.add_section( + description='''#### SpecEvalue Description + SpecEvalue : Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue). + ''', + plot=SpecE_bar_html + ) - self.add_section( - description='''#### xcorr description - * xcorr : cross-correlation scores, the search score of Comet. The value used for plotting is xcorr. - ''', - plot=xcorr_bar_html - ) + if xcorr_bar_html != '': + self.add_section( + description='''#### xcorr description + xcorr : cross-correlation scores, the search score of Comet. The value used for plotting is xcorr. + ''', + plot=xcorr_bar_html + ) - self.add_section( - description='''#### hyperscore description - * hyperscore : Hyperscore, the search score of Sage. The value used for plotting is hyperscore. - ''', - plot=hyper_bar_html - ) + if hyper_bar_html != '': + self.add_section( + description='''#### hyperscore description + hyperscore : Hyperscore, the search score of Sage. The value used for plotting is hyperscore. + ''', + plot=hyper_bar_html + ) # Create PEPs summary plot PEP_pconfig = { @@ -975,9 +978,7 @@ def draw_search_engine(self): PEP_bar_html = bargraph.plot(list(self.search_engine['PEPs'].values()), PEP_cats, PEP_pconfig) self.add_section( - description='''#### Summary of Posterior Error Probabilities - * PEP : Posterior Error Probability - ''', + description='''#### Summary of Posterior Error Probabilities (PEP)''', plot=PEP_bar_html ) # Create identified number plot @@ -992,22 +993,22 @@ def draw_search_engine(self): 'tt_decimals': 0, 'data_labels': self.search_engine['data_label']['consensus_label'], } - consensus_bar_html = bargraph.plot(list(self.search_engine['consensus_support'].values()), PEP_cats, - consensus_pconfig) - - self.add_section( - description='''#### Summary of consensus support for PSMs - Consensus support is a measure of agreement between search engines. Every peptide sequence in the analysis has been - identified by at least one search run. The consensus support defines which fraction (between 0 and 1) of the remaining - search runs "supported" a peptide identification that was kept. The meaning of "support" differs slightly between - algorithms: For best, worst, average and rank, each search run supports peptides that it has also identified among its - top considered_hits candidates. So the "consensus support" simply gives the fraction of additional search engines that - have identified a peptide. (For example, if there are three search runs, peptides identified by two of them will have a - "support" of 0.5.) For the similarity-based algorithms PEPMatrix and PEPIons, the "support" for a peptide is the average - similarity of the most-similar peptide from each (other) search run. - ''', - plot=consensus_bar_html - ) + # consensus_bar_html = bargraph.plot(list(self.search_engine['consensus_support'].values()), PEP_cats, + # consensus_pconfig) + # + # self.add_section( + # description='''#### Summary of consensus support for PSMs + # Consensus support is a measure of agreement between search engines. Every peptide sequence in the analysis has been + # identified by at least one search run. The consensus support defines which fraction (between 0 and 1) of the remaining + # search runs "supported" a peptide identification that was kept. The meaning of "support" differs slightly between + # algorithms: For best, worst, average and rank, each search run supports peptides that it has also identified among its + # top considered_hits candidates. So the "consensus support" simply gives the fraction of additional search engines that + # have identified a peptide. (For example, if there are three search runs, peptides identified by two of them will have a + # "support" of 0.5.) For the similarity-based algorithms PEPMatrix and PEPIons, the "support" for a peptide is the average + # similarity of the most-similar peptide from each (other) search run. + # ''', + # plot=consensus_bar_html + # ) else: self.add_section( description='''#### Summary of consensus PSMs