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aokad committed Jan 23, 2017
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49 changes: 22 additions & 27 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -57,27 +57,27 @@ For example, (using sample data)
cd {paplot install directory}
# create bar graphs of qc
paplot qc "example/qc/*.csv" ~/tmp DUMMY --config_file example/example.cfg
paplot qc "example/qc/SAMPLE*" ./demo demo --config_file ./example/example.cfg
# create bundle graphs of Structural Variation (SV)
paplot sv "example/sv/*.txt" ~/tmp DUMMY --config_file example/example.cfg
paplot ca "example/sv/SAMPLE*" ./demo demo --config_file ./example/example.cfg
# create sample-mutation plot (Mutation Matrix)
paplot mutation example/mutation/sample_merge.csv ~/tmp DUMMY --config_file example/example.cfg
paplot mutation example/mutation/sample_merge.csv ./demo demo --config_file ./example/example.cfg
# create signature plot (Mutation Matrix)
paplot signature example/signature/output_data.json ./demo demo 10 --config_file ./example/example.cfg
# create signature plot
paplot signature "example/signature/Nik_Zainal_2012.full.*.json" ./demo demo --config_file ./example/example.cfg
# create pmsignature plot (see https://github.com/friend1ws/pmsignature)
paplot pmsignature example/pmsignature/output_data.json ./demo demo 9 --config_file ./example/example.cfg
paplot pmsignature "example/pmsignature/Nik_Zainal_2012.ind.*.json" ./demo demo --config_file ./example/example.cfg
```

## 6. Description

```
$ paplot -h
usage: paplot [-h] [--version]
{conf,index,qc,ca,mutation,signature,pmsignature} ...
{conf,index,qc,ca,mutation,signature,pmsignature} ...
positional arguments:
{conf,index,qc,ca,mutation,signature,pmsignature}
Expand All @@ -99,9 +99,9 @@ optional arguments:
```
$ paplot qc -h
usage: paplot qc [-h] [--config_file CONFIG_FILE] [--title TITLE]
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
positional arguments:
input input files path
Expand All @@ -123,9 +123,9 @@ optional arguments:
```
$ paplot ca -h
usage: paplot ca [-h] [--config_file CONFIG_FILE] [--title TITLE]
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
positional arguments:
input input files path
Expand All @@ -147,9 +147,9 @@ optional arguments:
```
$ paplot mutation -h
usage: paplot mutation [-h] [--config_file CONFIG_FILE] [--title TITLE]
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
positional arguments:
input input files path
Expand All @@ -171,15 +171,14 @@ optional arguments:
```
$ paplot signature -h
usage: paplot signature [-h] [--config_file CONFIG_FILE] [--title TITLE]
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--sub_text SUB_TEXT] [--remarks REMARKS]
input output_dir project_name sig_num
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
positional arguments:
input input files path
output_dir output file path
project_name project name
sig_num signature number
optional arguments:
-h, --help show this help message and exit
Expand All @@ -188,7 +187,6 @@ optional arguments:
--title TITLE report's title
--ellipsis ELLIPSIS report file's ID
--overview OVERVIEW overview about report file
--sub_text SUB_TEXT sub text for each signature
--remarks REMARKS optional text
```

Expand All @@ -199,15 +197,14 @@ About pmsignaute?, see https://github.com/friend1ws/pmsignature)
```
$ paplot pmsignature -h
usage: paplot pmsignature [-h] [--config_file CONFIG_FILE] [--title TITLE]
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--sub_text SUB_TEXT] [--remarks REMARKS]
input output_dir project_name sig_num
[--ellipsis ELLIPSIS] [--overview OVERVIEW]
[--remarks REMARKS]
input output_dir project_name
positional arguments:
input input files path
output_dir output file path
project_name project name
sig_num signature number
optional arguments:
-h, --help show this help message and exit
Expand All @@ -216,9 +213,7 @@ optional arguments:
--title TITLE report's title
--ellipsis ELLIPSIS report file's ID
--overview OVERVIEW overview about report file
--sub_text SUB_TEXT sub text for each signature
--remarks REMARKS optional text
```

## 7. Tree of output directory
Expand Down
6 changes: 4 additions & 2 deletions example/example.cfg
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Expand Up @@ -229,7 +229,7 @@ tooltip_format3 = r2: {read_length_r2: ,}
###################### signature
[signature]
tooltip_format_signature_title = {sig}
tooltip_format_signature_partial = {route}: {#sum_item_value:.2}
tooltip_format_signature_partial = {route}: {#sum_item_value:6.2}
tooltip_format_mutation_title = {id}
tooltip_format_mutation_partial = {sig}: {#sum_item_value:.2}

Expand All @@ -248,7 +248,7 @@ background = True
key_id = id
key_mutation = mutation
key_signature = signature

key_mutation_count = mutation_count

###################### pmsignature
[pmsignature]
Expand Down Expand Up @@ -281,3 +281,5 @@ key_mutation = mutation
key_ref = ref
key_alt = alt
key_strand = strand
key_mutation_count = mutation_count

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