Mutational Signature レポート

ここでは、サンプルデータ [*] を使用して、Mutational Signature レポートを出力するために必要な入力データと設定方法を解説します。

[*]サンプルデータは paplot をダウンロードして解凍したディレクトリ中、example ディレクトリにあります。

Mutaitonal Signature 実行手順 に従いデータを準備する場合、設定ファイルの変更は必要ありません。

1. jsonフォーマット

paplotで Mutational Signature レポートを作成するためには Mutation Matrix レポートや Chromosomal Aberration レポート、QC レポートとは異なり、jsonファイル形式で変異シグネチャのデータを用意する必要があります。

ここでは、paplotが使用する変異シグネチャのデータフォーマットについて解説します。

exampleのデータファイルをテキストエディタで開くと次のようになっています。(長いため一部省略しています)

example/signature_stack/data2.json
{
  "signature":[
                [ # signature 1
                  [0.0018,0.0003,0.0002,0.0005,0.0014,0.0008,0.0002,0.0007,0.0012,0.0003,0.0002,0.0004,0.0271,0.0107,0.0016,0.0145],  # C -> A
                  [0.0023,0.0007,0.0001,0.002,0.0027,0.0005,0.0004,0.0032,0.0007,0.0004,0.0001,0.0013,0.1546,0.0306,0.0055,0.1931],   # C -> G
                  [0.0043,0.0016,0.0027,0.0019,0.0096,0.0026,0.0046,0.0053,0.0045,0.0021,0.0034,0.0028,0.2612,0.0517,0.0284,0.1335],  # C -> T
                  [0.0012,0.0007,0.0004,0.0003,0.0003,0.0003,0,0,0.0003,0.0001,0.0003,0,0.0005,0.0001,0.0001,0.0002],                 # T -> A
                  [0.0008,0.0003,0.0008,0.0007,0.0002,0.0004,0.0009,0.0005,0.0004,0.0003,0.0006,0.0003,0.0003,0.0004,0.0002,0.0004],  # T -> C
                  [0.0001,0.0001,0.0001,0.0001,0,0.0001,0.0001,0,0.0001,0.0001,0.0009,0.0002,0.0001,0,0.0001,0.0005]                  # T -> G
                ],
                [ # signature 2
                  [0.0266,0.0222,0.0026,0.02,0.0205,0.0145,0.0012,0.0155,0.0155,0.0094,0.0009,0.011,0.0224,0.0177,0.0019,0.0307],
                  [0.0127,0.0079,0.0035,0.0145,0.0058,0.0048,0.0015,0.0115,0.0034,0.0032,0,0.0071,0.0047,0.0145,0.0006,0.0246],
                  [0.0232,0.0099,0.042,0.0184,0.014,0.0108,0.0219,0.02,0.0137,0.0102,0.0264,0.0128,0.0048,0.0186,0.0153,0.0165],
                  [0.0096,0.0084,0.0094,0.0175,0.0075,0.0076,0.0046,0.0123,0.0044,0.0035,0.0028,0.008,0.0176,0.0047,0.0031,0.0139],
                  [0.0245,0.0087,0.0144,0.0235,0.0098,0.0096,0.0051,0.0102,0.0105,0.0053,0.0042,0.0108,0.0114,0.0081,0.0038,0.0098],
                  [0.0046,0.0006,0.0036,0.0035,0.0025,0.0009,0.0028,0.0082,0.0023,0.0005,0.004,0.0048,0.0041,0.0012,0.0056,0.0104]
                ]
              ],
  "id":["PD3851a","PD3890a","PD3904a"],
  "mutation":[[0,0,0.0594],[0,1,0.7677],[0,2,0.1727],[1,0,0.1474],[1,1,0.4064],[1,2,0.4461]],
  "mutation_count":[4001,7174,5804]
}

Mutational Signature レポートを作成するためのデータ要素

signature:
変異パターンの確率値です。
各変異シグネチャごと、置換パターン ("C > A" 等) ごと、コンテキスト ("TpCpA > TpApA" 等) ごとにそれぞれの値を記入します。
base の数は 3 か 5 のどちらかを設定できますが、混在させることはできません。
base とは、変異の位置 (N) を基準として、前後の塩基の数を意味します。base が 3 である場合、前後の塩基の数はそれぞれ 1 つです。base が 5 である場合、前後の塩基の数はそれぞれ 2 つです。

サンプルデータの base は 3 であり、コンテキストとして、次の並び順に 16 ケースの値を記述しています。

ANA,ANC,ANG,ANT,CNA,CNA,CNG,CNT,GNA,GNC,GNG,GNT,TNA,TNA,TNG,TNT

もし base を 5 にする場合は、次の順に 256 ケースの記述が必要です。

AANAA,AANAC,AANAG,AANAT,AANCA,AANCC,AANCG,AANCT,AANGA,AANGC,AANGG,AANGT,AANTA,AANTC,AANTG,AANTT,
ACNAA,ACNAC,ACNAG,ACNAT,ACNCA,ACNCC,ACNCG,ACNCT,ACNGA,ACNGC,ACNGG,ACNGT,ACNTA,ACNTC,ACNTG,ACNTT,
AGNAA,AGNAC,AGNAG,AGNAT,AGNCA,AGNCC,AGNCG,AGNCT,AGNGA,AGNGC,AGNGG,AGNGT,AGNTA,AGNTC,AGNTG,AGNTT,
ATNAA,ATNAC,ATNAG,ATNAT,ATNCA,ATNCC,ATNCG,ATNCT,ATNGA,ATNGC,ATNGG,ATNGT,ATNTA,ATNTC,ATNTG,ATNTT,
CANAA,CANAC,CANAG,CANAT,CANCA,CANCC,CANCG,CANCT,CANGA,CANGC,CANGG,CANGT,CANTA,CANTC,CANTG,CANTT,
CCNAA,CCNAC,CCNAG,CCNAT,CCNCA,CCNCC,CCNCG,CCNCT,CCNGA,CCNGC,CCNGG,CCNGT,CCNTA,CCNTC,CCNTG,CCNTT,
CGNAA,CGNAC,CGNAG,CGNAT,CGNCA,CGNCC,CGNCG,CGNCT,CGNGA,CGNGC,CGNGG,CGNGT,CGNTA,CGNTC,CGNTG,CGNTT,
CTNAA,CTNAC,CTNAG,CTNAT,CTNCA,CTNCC,CTNCG,CTNCT,CTNGA,CTNGC,CTNGG,CTNGT,CTNTA,CTNTC,CTNTG,CTNTT,
GANAA,GANAC,GANAG,GANAT,GANCA,GANCC,GANCG,GANCT,GANGA,GANGC,GANGG,GANGT,GANTA,GANTC,GANTG,GANTT,
GCNAA,GCNAC,GCNAG,GCNAT,GCNCA,GCNCC,GCNCG,GCNCT,GCNGA,GCNGC,GCNGG,GCNGT,GCNTA,GCNTC,GCNTG,GCNTT,
GGNAA,GGNAC,GGNAG,GGNAT,GGNCA,GGNCC,GGNCG,GGNCT,GGNGA,GGNGC,GGNGG,GGNGT,GGNTA,GGNTC,GGNTG,GGNTT,
GTNAA,GTNAC,GTNAG,GTNAT,GTNCA,GTNCC,GTNCG,GTNCT,GTNGA,GTNGC,GTNGG,GTNGT,GTNTA,GTNTC,GTNTG,GTNTT,
TANAA,TANAC,TANAG,TANAT,TANCA,TANCC,TANCG,TANCT,TANGA,TANGC,TANGG,TANGT,TANTA,TANTC,TANTG,TANTT,
TCNAA,TCNAC,TCNAG,TCNAT,TCNCA,TCNCC,TCNCG,TCNCT,TCNGA,TCNGC,TCNGG,TCNGT,TCNTA,TCNTC,TCNTG,TCNTT,
TGNAA,TGNAC,TGNAG,TGNAT,TGNCA,TGNCC,TGNCG,TGNCT,TGNGA,TGNGC,TGNGG,TGNGT,TGNTA,TGNTC,TGNTG,TGNTT,
TTNAA,TTNAC,TTNAG,TTNAT,TTNCA,TTNCC,TTNCG,TTNCT,TTNGA,TTNGC,TTNGG,TTNGT,TTNTA,TTNTC,TTNTG,TTNTT

寄与度グラフ描画データ

この項目はオプションです。

寄与度グラフは、各変異シグネチャに関連づけられている変異はどれくらいの数かを示す積み上げグラフです。 入力 json ファイルに id, mutation, mutation_count が設定されている場合、サンプル毎に変異シグネチャの寄与度グラフ ( 例 ) を作成します。

id:
サンプル名のリストです。
mutation_count:
サンプルごとの変異数です。
上記の例の場合、PD3851a の変異数=4001、PD3890a の変異数=7174、PD3904a の変異数=5804 となります。
mutation:
サンプルごと、変異シグネチャごとの割合を設定します。
[sample index, signature index, value] の順に記載します。

sample index は id で記載した順に 0 からカウントします。
上記の例の場合の sample index は PD3851a=0、PD3890a=1、PD3904a=2 となります。

signature index は signature で記載した順に 0 からカウントします。
上記の例の場合の signature index は signature1 = 0、signature2 = 1、background = 2 となります。

注釈

キーは変更可能です。キーを変更した場合は設定ファイル ([result_format_signature] セクションの key_* オプション) を変更してください。

example/signature_stack/paplot.cfg
[result_format_signature]
# json ファイルのキー
key_signature = signature
key_id = id
key_mutation = mutation
key_mutation_count = mutation_count

注釈

json ファイルの確認

paplot は python の json パッケージを使用しているため、次のコマンドで読めれば OK です。

json パッケージを使用したファイル確認例 (ファイル名が "data2.json" の場合)

$ python
>>> import json
>>> json.load(open("data2.json"))

2. 最小データセット

このセクションで生成するレポートを見る
このセクションで使用するデータセットを見る
このセクションで使用するデータセットをダウンロードする

入力データ形式は 1. jsonフォーマット 参照。

Mutaitonal Signature 実行手順 の手順でデータの準備を行う場合、設定ファイルの変更は必要ありません。

データファイル (変異シグネチャ数は 2)

example/signature_minimal/data.json
{
  "signature":[
    # signature 1
    [
      [0.0021,0.0006,0.0002,0.0007,0.0017,0.001,0.0003,0.0009,0.0014,0.0006,0.0003,0.0006,0.027,0.0108,0.0016,0.0147],
      [0.0025,0.0009,0.0002,0.0022,0.0029,0.0007,0.0005,0.0034,0.0009,0.0006,0.0002,0.0014,0.1504,0.0301,0.0053,0.1884],
      [0.0046,0.0018,0.0031,0.0021,0.0097,0.0029,0.0049,0.0055,0.0047,0.0024,0.0037,0.003,0.2557,0.0513,0.0286,0.1312],
      [0.0014,0.0009,0.0007,0.0006,0.0004,0.0005,0.0003,0.0003,0.0004,0.0003,0.0005,0.0002,0.0008,0.0003,0.0003,0.0005],
      [0.001,0.0004,0.0011,0.001,0.0003,0.0007,0.0012,0.0008,0.0006,0.0004,0.0007,0.0005,0.0005,0.0007,0.0004,0.0007],
      [0.0003,0.0003,0.0003,0.0003,0.0001,0.0003,0.0003,0.0003,0.0002,0.0002,0.0011,0.0004,0.0003,0.0002,0.0003,0.0009]
    ],
    # signature 2
    [
      [0.022,0.0183,0.0028,0.0171,0.0192,0.0148,0.0026,0.0157,0.0143,0.0108,0.0018,0.0116,0.0181,0.016,0.0021,0.0246],
      [0.0133,0.0088,0.0037,0.0136,0.0095,0.008,0.003,0.0131,0.0065,0.0063,0.0016,0.0095,0.0044,0.0135,0.0016,0.0171],
      [0.0195,0.0098,0.0283,0.0159,0.0138,0.0112,0.0156,0.0183,0.0128,0.0108,0.0186,0.0127,0,0.0146,0.0095,0.0115],
      [0.0095,0.0085,0.0102,0.0155,0.0077,0.0102,0.0096,0.0135,0.0054,0.0052,0.0058,0.0089,0.0145,0.0076,0.0058,0.016],
      [0.0192,0.0089,0.0135,0.0198,0.0089,0.0113,0.0092,0.0117,0.0092,0.0063,0.0064,0.01,0.0107,0.0096,0.0061,0.0123],
      [0.0059,0.0028,0.0068,0.0063,0.0039,0.0044,0.0076,0.0101,0.004,0.0028,0.007,0.0064,0.006,0.0046,0.008,0.0132]
    ]
  ]
}

設定ファイル

example/signature_minimal/paplot.cfg
[signature]
tooltip_format_signature_title = {sig}
tooltip_format_signature_partial = {route}: {#sum_item_value:6.2}

signature_y_max = -1

alt_color_CtoA = #1BBDEB
alt_color_CtoG = #211D1E
alt_color_CtoT = #E62623
alt_color_TtoA = #CFCFCF
alt_color_TtoC = #ACD577
alt_color_TtoG = #EDC7C4

[result_format_signature]
format = json
background = False
key_signature = signature

paplot を実行します。

paplot signature signature_minimal/data.json ./tmp signature_minimal \
--config_file ./signature_minimal/paplot.cfg

上記のコマンドを実行すると以下の場所にレポートが作成されます。

ここで出力されるレポートファイルの名称 graph_signature2.html には変異シグネチャ数が反映されています。

変異シグネチャ数は paplot 実行時に入力データ (data.json) から paplot が読み取ります。

./tmp
  ┗ signature_minimal
      ┗ graph_signature2.html

3. 複数データファイルの変異シグネチャ

このセクションで生成するレポートを見る
このセクションで使用するデータセットを見る
このセクションで使用するデータセットをダウンロードする

入力データ形式は 1. jsonフォーマット 参照。

Mutaitonal Signature 実行手順 の手順でデータの準備を行う場合、設定ファイルの変更は必要ありません。

変異シグネチャ解析においては、クラスタリング数を 2 や 3 などに固定せず、2 ～ 6 など幅を持たせた数で試験的に解析を行い、結果をみて適切なクラスタ数を決定することがあります。

今回のセクションでは、変異シグネチャのデータファイルを複数使用します。

今回の場合、以下のファイル構成になります。

example/signature_multi_class/

   # データファイル
  ┣ data2.json  # signature num = 2
  ┣ data3.json  # signature num = 3
  ┣ data4.json  # signature num = 4
  ┣ data5.json  # signature num = 5
  ┣ data6.json  # signature num = 6

   # 設定ファイル
  ┗ paplot.cfg

変異シグネチャのデータファイルごとに paplot を実行します。

paplot signature signature_multi_class/data2.json ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

paplot signature signature_multi_class/data3.json ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

paplot signature signature_multi_class/data4.json ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

paplot signature signature_multi_class/data5.json ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

paplot signature signature_multi_class/data6.json ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

下記のようにまとめて実行することもできます。

paplot signature "signature_multi_class/data*.json" ./tmp signature_multi_class \
--config_file ./signature_multi_class/paplot.cfg

上記のコマンドを実行すると以下の場所にレポートが作成されます。

ここで出力されるレポートファイルの名称 graph_signature2.html には変異シグネチャ数が反映されています。

変異シグネチャ数は paplot 実行時に入力データ (data.json) から paplot が読み取ります。

./tmp
  ┗ signature_multi_class
      ┣ graph_signature2.html
      ┣ graph_signature3.html
      ┣ graph_signature4.html
      ┣ graph_signature5.html
      ┗ graph_signature6.html

4. 寄与度グラフ

このセクションで生成するレポートを見る
このセクションで使用するデータセットを見る
このセクションで使用するデータセットをダウンロードする

レポートに変異の内訳グラフを追加します。 Mutaitonal Signature 実行手順 によりデータの準備を行う場合、あらかじめ出力するように設定しています。

入力データ形式は 1. jsonフォーマット 参照。

複数データ実行方法は 3. 複数タイプの変異シグネチャ 参照。

paplot を実行します。

paplot signature "signature_stack/data*.json" ./tmp signature_stack \
--config_file ./signature_stack/paplot.cfg