Update TP53 pipeline analysis (greenelab#86)

* remove args from within disease

remove checkpoint call from tp53 viz

remove checkpoint and convert to pdf

update copy burden analysis

add two additional notebook scripts for tp53 analysis

remove old figure generation script

update name of supplementary figure plot0

update gzip copy burden figures

add back l1 mixing parameter

* remove extra new line

add tp53 exon processing notebook

make snaptron bash executable

adding updated snaptron results

add processing exons notebook

rerun pipeline and generate junction gz

convert from svg to pdf

also swith single quotes to double

update file name

* update sample freeze file input to tp53 notebook

update phenocopy tp53 sample freeze

* update phenocopying results

rerun pipeline to update existing results

add all TP53 classifier results

rerun pipeline

rerun pipeline and add results outside classifiers folder

rerun pipeline again

classifiers/TP53/classifier_summary.txt

@@ -0,0 +1,61 @@
+Parameters:
+Genes:	TP53
+Diseases:	BLCA	BRCA	CESC	COAD	ESCA	GBM	HNSC	KICH	LGG	LIHC	LUAD	LUSC	PAAD	PRAD	READ	SARC	SKCM	STAD	UCEC
+Alternative Genes:	None
+Alternative Diseases:	Auto
+Number of Features:	8034
+Drop Gene:	True
+Copy Number:	True
+Alphas:	0.1	0.13	0.15	0.18	0.2	0.3	0.4	0.6	0.7
+L1_ratios:	0.1	0.125	0.15	0.2	0.25	0.3	0.35
+Hypermutated Removed:	True
+
+Results:
+Optimal Alpha:	0.1
+Optimal L1:	0.1
+Coefficients:	classifiers/TP53/classifier_coefficients.tsv
+Training AUROC:	0.9340136200170487
+Testing AUROC:	0.9339535941334193
+Cross Validation AUROC	0.915645902972101
+Training AUPR:	0.9027559509594195
+Testing AUPR:	0.9004359151957726
+Cross Validation AUPR:	0.8737165659342406
+Disease specific performance:
+	BLCA	Training AUROC:	0.908662900188324	Testing AUROC:	0.9026315789473685	Cross Validation AUROC:	0.8647964153516461
+	BRCA	Training AUROC:	0.9596716428092276	Testing AUROC:	0.9478458049886621	Cross Validation AUROC:	0.9430661830750514
+	CESC	Training AUROC:	0.717351598173516	Testing AUROC:	0.6666666666666667	Cross Validation AUROC:	0.6518264840182649
+	COAD	Training AUROC:	0.9305714649357261	Testing AUROC:	0.9848484848484849	Cross Validation AUROC:	0.9129438717067583
+	ESCA	Training AUROC:	0.675839552238806	Testing AUROC:	0.9	Cross Validation AUROC:	0.6417910447761195
+	GBM	Training AUROC:	0.879378837125316	Testing AUROC:	0.96875	Cross Validation AUROC:	0.8671000361141207
+	HNSC	Training AUROC:	0.8875140607424072	Testing AUROC:	0.7352941176470589	Cross Validation AUROC:	0.8598783106657122
+	KICH	Training AUROC:	0.8565789473684211	Testing AUROC:	1.0	Cross Validation AUROC:	0.7657894736842106
+	LGG	Training AUROC:	0.973224297258632	Testing AUROC:	1.0	Cross Validation AUROC:	0.9670378533039478
+	LIHC	Training AUROC:	0.9328933423258503	Testing AUROC:	1.0	Cross Validation AUROC:	0.9037479525965892
+	LUAD	Training AUROC:	0.9104161558522613	Testing AUROC:	0.8573913043478261	Cross Validation AUROC:	0.8901321801930322
+	LUSC	Training AUROC:	0.7090379008746356	Testing AUROC:	0.575187969924812	Cross Validation AUROC:	0.6619869925992374
+	PAAD	Training AUROC:	0.8886446886446886	Testing AUROC:	0.86	Cross Validation AUROC:	0.8192918192918193
+	PRAD	Training AUROC:	0.8624234200896345	Testing AUROC:	0.9825783972125435	Cross Validation AUROC:	0.8068747173224785
+	READ	Training AUROC:	0.9264705882352942	Testing AUROC:	1.0	Cross Validation AUROC:	0.8998599439775911
+	SARC	Training AUROC:	0.8400537634408602	Testing AUROC:	0.7416666666666667	Cross Validation AUROC:	0.8057795698924731
+	SKCM	Training AUROC:	0.9319999999999999	Testing AUROC:	0.927536231884058	Cross Validation AUROC:	0.9167619047619049
+	STAD	Training AUROC:	0.9240064446831364	Testing AUROC:	0.9307958477508651	Cross Validation AUROC:	0.907312925170068
+	UCEC	Training AUROC:	0.9421921921921922	Testing AUROC:	0.9951923076923077	Cross Validation AUROC:	0.9375721875721875
+	BLCA	Training AUPR:	0.9016969301453566	Testing AUPR:	0.8290129945285417	Cross Validation AUPR:	0.8455558343213506
+	BRCA	Training AUPR:	0.9160947686393439	Testing AUPR:	0.9194046974481075	Cross Validation AUPR:	0.8792974978397354
+	CESC	Training AUPR:	0.4137247471157805	Testing AUPR:	0.5555555555555556	Cross Validation AUPR:	0.34319186079556907
+	COAD	Training AUPR:	0.9231127810137119	Testing AUPR:	0.9907216297825174	Cross Validation AUPR:	0.8973406250362697
+	ESCA	Training AUPR:	0.9045602637629551	Testing AUPR:	0.9866269841269841	Cross Validation AUPR:	0.8997814791526315
+	GBM	Training AUPR:	0.8319781560827086	Testing AUPR:	0.95	Cross Validation AUPR:	0.833207777068663
+	HNSC	Training AUPR:	0.9303436707739461	Testing AUPR:	0.8472350938025608	Cross Validation AUPR:	0.9056878391985403
+	KICH	Training AUPR:	0.8296838129417035	Testing AUPR:	1.0	Cross Validation AUPR:	0.6301928679590945
+	LGG	Training AUPR:	0.9727474272401524	Testing AUPR:	1.0	Cross Validation AUPR:	0.9685580008970107
+	LIHC	Training AUPR:	0.874386286443685	Testing AUPR:	1.0	Cross Validation AUPR:	0.8128001331254809
+	LUAD	Training AUPR:	0.8866983603438293	Testing AUPR:	0.8256994547890552	Cross Validation AUPR:	0.8444501537052753
+	LUSC	Training AUPR:	0.907204990292803	Testing AUPR:	0.8780694320440617	Cross Validation AUPR:	0.8846791118453962
+	PAAD	Training AUPR:	0.9427279611038916	Testing AUPR:	0.9272546897546897	Cross Validation AUPR:	0.8950906607275801
+	PRAD	Training AUPR:	0.5451147707966071	Testing AUPR:	0.8954648526077098	Cross Validation AUPR:	0.4616270021084826
+	READ	Training AUPR:	0.9551215222701015	Testing AUPR:	1.0	Cross Validation AUPR:	0.9426077963650131
+	SARC	Training AUPR:	0.7499328066984672	Testing AUPR:	0.735546398046398	Cross Validation AUPR:	0.715376575572616
+	SKCM	Training AUPR:	0.7270939999724422	Testing AUPR:	0.6666666666666667	Cross Validation AUPR:	0.6622860457186759
+	STAD	Training AUPR:	0.9065930651336558	Testing AUPR:	0.9344380869034848	Cross Validation AUPR:	0.8910930627008757
+	UCEC	Training AUPR:	0.9129843619570152	Testing AUPR:	0.9930555555555556	Cross Validation AUPR:	0.9103680009676541