def proportionalityCorrelationPlots(D, measure, methods, simIDs, outdir, plotname): sns.set_style('white') sns.set_context('poster') plt.clf() plt.cla() md = {} for m in methods: md[m] = [] for i in simIDs: pc = AnalysisUtils.proportionalityCorrelation( "{}_truth{}".format(measure, str(i)), "{}_{}{}".format(measure, m, str(i)), D) md[m].append(pc) ax = None for mn, mv in md.items(): weights = np.ones_like(mv)/len(mv) ax = sns.distplot(mv, hist_kws={"histtype": "stepfilled"}, kde=False, rug=True, label=mn, ax=ax, norm_hist=False) sns.despine() ax = plt.axes() ax.set_xlabel('proportionality correlation') ax.set_ylabel('frequency') plt.legend() plt.savefig('{}/{}.pdf'.format(outdir, plotname))
def makeTable(methodDict, outpath, outfile, measure, annotPath): import pandas as pd import seaborn as sns import ParsingUtils import AnalysisUtils dframes = [] for k, v in methodDict.items(): if k.upper().startswith('SALMON'): d = ParsingUtils.readSalmon(v, '_{}'.format(k)) elif k.upper().startswith('KALLISTO'): d = ParsingUtils.readKallisto(v, '_{}'.format(k)) elif k.upper().startswith('EXPRESS'): d = ParsingUtils.readExpress(v, '_{}'.format(k)) elif k.upper() == 'SAILFISH': d = ParsingUtils.readSailfish(v, '_{}'.format(k)) elif k.upper() == 'SAILFISH (QUASI)': d = ParsingUtils.readSalmon(v, '_{}'.format(k)) elif k.upper().startswith('TRUTH'): suffix = '_{}'.format(k) d = ParsingUtils.readProFile(v, suffix) d["TPM{}".format(suffix)] = 1000000.0 * (d["ExpFrac{}".format(suffix)] / d["ExpFrac{}".format(suffix)].sum()) # Flux sim thinks paired-end = 2 reads . . . sinh d["NumReads{}".format(suffix)] = d["SeqNum{}".format(suffix)] * 0.5 # Add this dataframe to the list dframes.append(d) M = dframes[0].join(dframes[1:]) # Filter eXpress results minVal = np.inf for mn in set(methodDict.keys()) - set(["Truth", "eXpress"]): newMin = M.loc[M["{}_{}".format(measure, mn)]>0, "{}_{}".format(measure,mn)].min() minVal = min(minVal, newMin) print("filtering eXpress results < {} {}".format(minVal, measure)) AnalysisUtils.filterValues("{}_{}".format(measure, "eXpress"), M, minVal) org = outfile.split('/')[-1].split('_')[0] print("org = {}".format(org)) if org == 'human': plotStratifiedDiffs(M, methodDict, annotPath, outpath, measure) mrdName = 'abs. mean rel. diff.' corrName = 'Spearman corr.' propName = 'Proportionality corr.' tpefName = 'TP error fraction' tpMedErrorName = 'TP median per. error' res = pd.DataFrame(data={ m : {tpMedErrorName : np.nan, tpefName : np.nan, mrdName : np.nan, corrName : np.nan, propName : np.nan} for m in (methodDict.keys() - set('Truth'))}) import scipy as sp import scipy.stats for k in methodDict: if k.upper() != "TRUTH": c = sp.stats.spearmanr(M["{}_Truth".format(measure)], M["{}_{}".format(measure, k)])[0] res[k][corrName] = c mrd, _ = AnalysisUtils.relDiff("{}_Truth".format(measure), "{}_{}".format(measure, k), M) res[k][mrdName] = mrd["relDiff"].abs().mean() pc = AnalysisUtils.proportionalityCorrelation("{}_Truth".format(measure), "{}_{}".format(measure, k), M) res[k][propName] = pc tpind = M[M["{}_Truth".format(measure)] >= 1] y = tpind["{}_{}".format(measure, k)] x = tpind["{}_Truth".format(measure)] ef = 10.0 re = (y - x) / x are = 100.0 * (y - x).abs() / x tpef = len(are[are > ef]) / float(len(are)) res[k][tpefName] = tpef res[k][tpMedErrorName] = re.median() res.drop('Truth', axis=1, inplace=True) print(res) res.to_csv(outfile+".csv") with open(outfile, 'w') as ofile: ofile.write(res.to_latex(float_format=lambda x: "{0:.2f}".format(x))) print("wrote {}".format(outpath))