From aba81444f0754f729eedd58ce1034c816bd30392 Mon Sep 17 00:00:00 2001 From: gwaygenomics Date: Wed, 10 Oct 2018 10:33:37 -0400 Subject: [PATCH] rerun pipeline and refresh results --- figures/NF1_confidence_scores.pdf | Bin 19722 -> 19722 bytes figures/NF1_predictions.pdf | Bin 19136 -> 19136 bytes figures/Ras_confidence_scores.pdf | Bin 28608 -> 28608 bytes figures/Ras_predictions.pdf | Bin 18118 -> 18118 bytes figures/TP53_confidence_scores.pdf | Bin 20832 -> 20832 bytes ...53_osteosarcoma_variant_classification.pdf | Bin 19759 -> 19759 bytes figures/TP53_predictions.pdf | Bin 18444 -> 18444 bytes figures/TP53_variant_classification.pdf | Bin 24747 -> 24747 bytes figures/classifier_precision_recall_curve.pdf | Bin 17155 -> 17155 bytes figures/classifier_roc_curve.pdf | Bin 15950 -> 15950 bytes figures/histology_NF1_predictions.pdf | Bin 38737 -> 38737 bytes figures/histology_Ras_predictions.pdf | Bin 41067 -> 41067 bytes figures/histology_TP53_predictions.pdf | Bin 41317 -> 41317 bytes html/2.evaluate-classifier-pdx.html | 171 ++++++++++++++++-- html/3.explore-variants.html | 8 +- 15 files changed, 161 insertions(+), 18 deletions(-) diff --git a/figures/NF1_confidence_scores.pdf b/figures/NF1_confidence_scores.pdf index e6aba3ebee00dfe47797b1281e7e48176d584c8c..959aa18131b0b4929c827a2ec5c9cc48b52151d8 100644 GIT binary patch delta 23 ecmeC0#n?5AaRavphoOO?fsvV^>1JV%?<@dTat7}J delta 23 ecmeC0#n?5AaRavphk=Qqsey^9@n&IwmGQt-#tk!FISdU94UEhT%r`G|m1hM2XYU7* delta 23 fcmX>wmGQt-#tk!FISfn;O$|&;OgArdm1hM2Xfg+v diff --git a/figures/Ras_confidence_scores.pdf b/figures/Ras_confidence_scores.pdf index 5234b894ffa235093f354833272d3fedc2b1b9fe..474fcd5edc8f6b08d02595bbe0cd1e01f90d9602 100644 GIT binary patch delta 23 fcmX?bpYgzb#tmOHI1CL84UEhTO*a3{ILrnBeys_{ delta 23 fcmX?bpYgzb#tmOHI1Ee-O$|&;jW_?zILrnBe)b8? diff --git a/figures/Ras_predictions.pdf b/figures/Ras_predictions.pdf index 85ada0220302ef4687847fca38b4bb6e8c78355d..be7cfc7a706632d18e6ea64fe4267eeeb1ae9141 100644 GIT binary patch delta 23 fcmX@s%XqApal?B@4nqS&10yp7^UdEK&$9pkZ+Hmc delta 23 fcmX@s%XqApal?B@4g(WIQv(wd)6L%<&$9pkZ@UQQ diff --git a/figures/TP53_confidence_scores.pdf b/figures/TP53_confidence_scores.pdf index c15833ef7cc9072849966628c239cfc8d263f7f6..86842583a1fd06cb523544145848045f3f3181f4 100644 GIT binary patch delta 23 ecmaE`i1EQ9#toJ}9EJvl21aIvrkfpo1Ivm$1DI=tOoP| diff --git a/figures/TP53_variant_classification.pdf b/figures/TP53_variant_classification.pdf index 1ec3ff5fe87e9306d27321fce5f0a8a3344aa6db..1117aa1b216e71dc54feee1cddffd6f24bdbf324 100644 GIT binary patch delta 23 fcmZ2|ka6`v#tl!RI1CL84UEhTO*g-Z+Rq9AbOi|> delta 23 fcmZ2|ka6`v#tl!RI1Ee-O$|&;O*X%Y+Rq9AbWRB+ diff --git a/figures/classifier_precision_recall_curve.pdf b/figures/classifier_precision_recall_curve.pdf index 0c18d4db0a5e18055a22a2a9bebb94cfc732f8b0..8a72266656846cc827f777031b2936bd2459e12b 100644 GIT binary patch delta 23 ecmZo}V{C3?+@NE}VQ64zU}R=sw%Nq)JPQC*pa#DH delta 23 ecmZo}V{C3?+@NE}VPIltYG7hwy4l3;JPQC*=?2CC diff --git a/figures/classifier_roc_curve.pdf b/figures/classifier_roc_curve.pdf index 226cfc3856618fc633191faf4624f16c86b6add7..c8a7efb9ab4c3fab286bfa6c1d475e6efcfc9c0a 100644 GIT binary patch delta 21 ccmX?CbFOAXvL%P1fuVtsnSt5nY|F( diff --git a/figures/histology_Ras_predictions.pdf b/figures/histology_Ras_predictions.pdf index 5051a3cc768289be64506ebd9395782acb64edb9..81d442a68434e724f4bf447ec2f543e0843be20b 100644 GIT binary patch delta 23 fcmaETfa&!CrVW3la~K*J8W@=wSZrpQkLoad Status MatrixLoad Status Matrix 
Missense_Mutation    112
 Shallow_Del           17
-Nonsense_Mutation     13
 Fusion                13
+Nonsense_Mutation     13
 Frame_Shift_Del        5
 Splice_Site            3
 Frame_Shift_Ins        3
-In_Frame_Del           1
 Deep_Del               1
+In_Frame_Del           1
 Name: Variant_Classification, dtype: int64
@@ -12150,18 +12150,18 @@

Load Status MatrixExtract Gene Status.assign(ras_status = full_status_df.loc[:, ras_genes] .max(axis='columns')) ) + +full_status_df.head() +
+
+ + +
+ +
Out[12]:
+ + + +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ModelALKBRAFCICDMDHRASKRASNF1NRASPTPN11SOS1TP53Histology_Fullras_status
0ALL-0310000000000MLL-ALL1
1ALL-0700000100000BCP-ALL1
2ALL-0800010000000T-ALL1
3ALL-10800000100000Ph-likeALL1
4ALL-11500000000001BCP-ALL0
+
+
+ +
+ +
+
+
@@ -12917,21 +13060,21 @@

Load Clinical Data InformationWrite output files for downs scores_file = os.path.join("results", "classifier_scores_with_clinical_and_alterations.tsv") genes = ras_genes + ['TP53'] -scores_df.drop(['Model_x', 'Model_y', 'Histology_Full'], axis='columns') +scores_df = scores_df.drop(['Model_x', 'Model_y', 'Histology_Full'], axis='columns') scores_df[genes] = scores_df[genes].fillna(value=0) scores_df.sort_values(by='sample_id').to_csv(scores_file, sep='\t', index=False) diff --git a/html/3.explore-variants.html b/html/3.explore-variants.html index 169d076..c04bffb 100644 --- a/html/3.explore-variants.html +++ b/html/3.explore-variants.html @@ -12007,13 +12007,13 @@

Output

Th RNA Part of PPTC Model Part of PPTC ... + HRAS KRAS NF1 NRAS PTPN11 SOS1 TP53 - Histology_Full ras_status tp53_status nf1_status @@ -12039,7 +12039,7 @@

Output

Th 0.0 0.0 0.0 - NaN + 0.0 0 0 0 @@ -12063,14 +12063,14 @@

Output

Th 0.0 0.0 0.0 - MLL-ALL + 0.0 1 0 0 -

2 rows × 42 columns

+

2 rows × 39 columns