From dbda821555f2e9293d824b7c3662d251c0004252 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Tue, 30 Oct 2012 17:47:13 -0500 Subject: Did some work converting show_trait.html to using bootstrap for styling --- wqflask/wqflask/templates/show_trait.html | 2558 +++++++++++++++-------------- 1 file changed, 1302 insertions(+), 1256 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index d48f9487..ab662a77 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1,1380 +1,1426 @@ +{% extends "base.html" %} +{% block title %}Trait Data and Analysis{% endblock %} +{% block content %} + +
+
+

{{ this_trait.symbol}}

+

+ {{ this_trait.name }}: {{ this_trait.description_fmt }} +

+
+
+ + + +
+
+

{{ this_trait.species.capitalize() }} - + {{ fd.RISet }} - + {{ this_trait.symbol }} + +

+
+ +
+
Aliases
+
{{ this_trait.alias_fmt }}
+ +
Location
+
{{ this_trait.location_fmt }}
+ +
Database
+
+ + {{ this_trait.database.name }} + +
+ +
+ + BLAT Specifity + +
+
{{ "%.1f" % (this_trait.probe_set_specificity) }}
+ +
BLAT Score
+
{{ "%i" % (this_trait.probe_set_blat_score) }}
+
+ + + + + + + -
  • Probability Plot
    • + + -
  • Bar Graph (by name)
    • + -
  • Bar Graph (by rank)
    • + -
  • Box Plot
    • - + -
    -
    +
    + {# + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #} + {% for key in hddn %} + + {% endfor %} +
    +
    + Trait Data and Analysis  for Record ID 1441186_at +
    +
    + +

      Details and Links

    + +

    + + + + + + + + + + + + + + + + + + + + + + - {% extends "base.html" %} - {% block title %}Trait Data and Analysis{% endblock %} - {% block content %} - - - + -
    Gene Symbol:{{ this_trait.symbol }}
    Aliases:{{ this_trait.alias_fmt }}
    Description:
    - - - -
    - - {# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #} - {% for key in hddn %} - - {% endfor %} -
    -
    - Trait Data and Analysis  for Record ID 1441186_at -
    -
    - -

      Details and Links

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + + - + + + + + + + + + + - - - - - - - - - - - - - -
    Gene Symbol:{{ this_trait.symbol }}
    Aliases:{{ this_trait.alias_fmt }}
    Description:{{ this_trait.description_fmt }}
    Location:{{ this_trait.location_fmt }}
    Target Score: - - - BLAT specificity - : {{ "%.1f" % (this_trait.probe_set_specificity) }}    - Score: {{ "%i" % (this_trait.probe_set_blat_score) }}   - -
    Species and Group:{{ this_trait.species.capitalize() }}, {{fd.RISet}}
    Database: - {{ this_trait.database.name }} -
    Resource Links:{{ this_trait.description_fmt }}
    Location: - - - - Gene - + {{ this_trait.location_fmt }}
    Target Score: + + + BLAT specificity + : {{ "%.1f" % (this_trait.probe_set_specificity) }}    + Score: {{ "%i" % (this_trait.probe_set_blat_score) }}   -   UniGene  GenBank  HomoloGene  
    UCSC  BioGPS  STRING  PANTHER  Gemma  SynDB  ABA  

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -- - Check probe locations at UCSC Write or review comments about this gene - View SNPs and Indels - View probes, SNPs, and RNA-seq at UTHSC - Check sequence of probes
    AddFindVerifyGeneWikiSNPsRNA-seqProbes
    - -

      Basic Statistics

    - - -

    Include: -
    -
    -
    -
    - +
    +     		{{ this_trait.species.capitalize() }}, {{fd.RISet}}
    - - + -
  • Probability Plot
    • + -
  • Bar Graph (by name)
    • + + -
  • Bar Graph (by rank)
    • + + + -
  • Box Plot
    • - + + -
    -
    - {% for sd in stats_data %} -
    -
    Database: + {{ this_trait.database.name }} +
    Resource Links:
    - - - -
    - - - + - - + + + + + + + + + + + + + + +
    StatisticValue
    + + + + Gene + + +   UniGene  GenBank  HomoloGene  
    UCSC  BioGPS  STRING  PANTHER  Gemma  SynDB  ABA  

    + + + + + + + + + + + + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    ++ + Check probe locations at UCSC Write or review comments about this gene + View SNPs and Indels
    N of Samples + View probes, SNPs, and RNA-seq at UTHSC + Check sequence of probes {{ sd.N }}
    Mean{{ "%2.3f" % sd.traitmean }}
    Median{{ "%2.3f" % sd.traitmedian }}
    Standard Error (SE){{ "%2.3f" % sd.traitsem }}
    Standard Deviation (SD){{ "%2.3f" % sd.traitstdev }}
    Minimum{{ "%2.3f" % sd.min }}
    Maximum{{ "%2.3f" % sd.max }}
    Range (log2){{ "%2.3f" % sd.range_log2 }}
    Range (fold){{ "%2.3f" % sd.range_fold }}
    Interquartile Range{{ "%2.3f" % sd.interquartile }}
    -
    - - -
    - - - - - - - - -
    nP_OE9u7BSx.gif

    -
    - This plot evaluates whether data are normally distributed. Different symbols represent different groups.
    -
    - More about Normal Probability Plots and more - about interpreting these plots from the glossary
    -
    - -
    - - - - -
    - Box_gUFtEOVI.gif - -

    More about Box Plots

    -
    -
    - -
    - - - - -
    Bar_y7L2rYlL.gif
    -
    - -
    - - - - -
    Bar_1Z4GjYFq.gif
    -
    - - {% endfor %} - {# Not used now - Todo: Delete after we're sure this is right. -
    -
    AddFindVerifyGeneWiki
    - - - -
    - - - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    StatisticSNPsValue
    RNA-seq
    N of SamplesProbes71
    Mean6.109
    Median6.084
    Standard Error (SE)0.022
    Standard Deviation (SD)0.187
    Minimum5.782
    Maximum6.579
    Range (log2)0.797
    Range (fold)1.74
    Interquartile Range1.13
    -
    -
    - -
    - - - - - - - - -
    nP_eSYO7ZQg.gif

    -
    - This plot evaluates whether data are normally distributed. Different symbols represent different groups.
    -
    - More about Normal Probability Plots and more - about interpreting these plots from the glossary
    -
    - -
    - - - - -
    - Box_PWNWQMfj.gif - -

    More about Box Plots

    -
    -
    - -
    - - - - -
    Bar_VuPqYbR6.gif
    -
    - -
    - - - - -
    Bar_9PbdvXZ9.gif
    -
    - + + + -
    +

      Basic Statistics

    - + + + - -
    + {% for sd in stats_data %} +
    +
      +
    • Basic Table
      • -
      - - - + -
      -
      - - - +
    • Probability Plot
      • - - +
    • Bar Graph (by name)
      • - - +
    • Bar Graph (by rank)
      • - - +
    • Box Plot
      • + - - +
      +
      StatisticValue
      N of Samples32
      Mean
      + + - -
      + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - -
      Statistic6.176
      Value
      Median
      N of Samples6.170
      {{ sd.N }}
      Standard Error (SE)
      Mean0.027
      {{ "%2.3f" % sd.traitmean }}
      Standard Deviation (SD)
      Median0.150
      {{ "%2.3f" % sd.traitmedian }}
      Minimum
      Standard Error (SE)5.906
      {{ "%2.3f" % sd.traitsem }}
      Maximum
      Standard Deviation (SD)6.485
      {{ "%2.3f" % sd.traitstdev }}
      Range (log2)
      Minimum0.579
      {{ "%2.3f" % sd.min }}
      Range (fold)
      Maximum1.49
      {{ "%2.3f" % sd.max }}
      Interquartile Range
      Range (log2)1.15
      -
      - +       		{{ "%2.3f" % sd.range_log2 }}
      - - - + + - - - -
      nP_swDAFlJy.gif
      Range (fold)

      -
      - This plot evaluates whether data are normally distributed. Different symbols represent different groups.
      -
      - More about Normal Probability Plots and more - about interpreting these plots from the glossary
      -
      - -
      - - - - -
      - Box_6sQJ8xhK.gif - -

      More about Box Plots

      -
      -
      - -
      - - - - -
      Bar_QMWE2VEp.gif
      -
      - -
      - - - - -
      Bar_X07QmgsX.gif
      -
      -
    -
    - #} + {{ "%2.3f" % sd.range_fold }} + -

      Calculate Correlations

    - -

    - - - - - -
    -
    -
    - - - - -
    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method: - -
    Database: - -
    Return:
    Samples: - -
    -
    -
    - Pearson -     - Spearman Rank -
    -
    - -

    - - - The Sample Correlation - is computed - between trait data and any
    - other traits in the sample database selected above. Use - Spearman - Rank
    - when the sample size is small (<20) or when there are influential outliers. -     - - - -
    -
    -
    -
    -
    + + Interquartile Range -

      Mapping Tools

    + {{ "%2.3f" % sd.interquartile }} + + + + + +
    -

    +

    More about Box Plots

    + + + + - - - - -
    -
    -
    + {% endfor %} + {# Not used now - Todo: Delete after we're sure this is right. +
    + +
  • Bar Graph (by name)
    • -
    - - - - - - - - -
    - - - +
  • Bar Graph (by rank)
    • - - -
    Chromosome: + + + +
    + + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - + + - - - + + - - + + - + +
    StatisticValue
    N of Samples71
    Mean6.109
    Median6.084
    Standard Error (SE)0.022
    Standard Deviation (SD)0.187
    Minimum5.782
    Maximum6.579
    Range (log2)0.797
    Range (fold)
    1.74
    Mapping Scale:
    Interquartile Range1.13
    +
    + - -

    - Permutation Test (n=2000)
    - Bootstrap Test (n=2000)
    - Use Parents
    - Use Weighted
    -
    -
    -
    -
    Interval Mapping computes linkage maps - for the entire genome or single
    - chromosomes. The Permutation Test estimates suggestive and - significant
    - linkage scores. The Bootstrap Test estimates the precision of the QTL - location.
    -
    - -
    - - - - - - - - -
    - - - - - - - - - - - - - - - - - - -
    Display LRS greater than:
    Display all LRS
    Use Parents
    Use Weighted

    -
    -
    -
    Marker regression computes and displays LRS - values for individual markers.
    - This function also lists additive effects (phenotype units per allele) and
    - dominance deviations for some datasets.

    -
    - -
    - - - - - - - - -
    - - - - - + +
    Chromosome: + + + + + + + +
    nP_eSYO7ZQg.gif

    +
    + This plot evaluates whether data are normally distributed. Different symbols represent different groups.
    +
    + More about Normal Probability Plots and more + about interpreting these plots from the glossary
    + - +
    + + + + +
    + Box_PWNWQMfj.gif - +

    More about Box Plots

    +
    +
    - +
    + + + + +
    Bar_VuPqYbR6.gif
    +
    - +
    + + + + +
    Bar_9PbdvXZ9.gif
    +
    + - +
    - - + - +
    + + + - - - - - -
    + + + - + + - + + - + + - + + - + + - + + - + + - - - + + - - + + - + - - - - - - - - - -
    StatisticValue
    N of Samples32
    Mean6.176
    Median6.170
    Standard Error (SE)
    Mapping Scale:0.027
    Standard Deviation (SD)
    Control Locus:

    - Permutation Test (n=2000)
    - Bootstrap Test (n=2000)
    - Use Parents
    -
    -
    -
    -
    Composite Interval Mapping allows you to control - for a single marker as
    - a cofactor. To find a control marker, run the Marker Regression function.
    -
    - -
    - - - + +
    - - - - - + - - - + + - - + + - + - + + - + + + + + + + + + + + + + + + + + +
    Sort by:0.150
    Minimum
    Return:5.906
    Maximum6.485
    Range (log2)0.579
    Range (fold)1.49
    Interquartile Range1.15
    +
    +
    + +
    + + + + + + + + +
    nP_swDAFlJy.gif

    +
    + This plot evaluates whether data are normally distributed. Different symbols represent different groups.
    +
    + More about Normal Probability Plots and more + about interpreting these plots from the glossary
    +
    + +
    + + + + +
    + Box_6sQJ8xhK.gif + +

    More about Box Plots

    +
    +
    + +
    + + + + +
    Bar_QMWE2VEp.gif
    +
    + +
    + + + + +
    Bar_X07QmgsX.gif
    +
    +
    +
    + #} + +

      Calculate Correlations

    + +

    + + + + + +
    +
    +
    + + + + +
    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Method: + +
    Database: + +
    Return:
    Samples: + +
    +
    +
    + Pearson +     + Spearman Rank +
    +
    + +

    + + + The Sample Correlation + is computed + between trait data and any
    + other traits in the sample database selected above. Use + Spearman + Rank
    + when the sample size is small (<20) or when there are influential outliers. +     + + + +
    +
    +
    +
    +
    + +

      Mapping Tools

    + +

    + + + + + +
    +
    + + +
    + + + + + + + + +
    + + + + + + + + + + + + +
    Chromosome:
    Mapping Scale:

    + Permutation Test (n=2000)
    + Bootstrap Test (n=2000)
    + Use Parents
    + Use Weighted
    +
    +
    +
    +
    Interval Mapping computes linkage maps + for the entire genome or single
    + chromosomes. The Permutation Test estimates suggestive and + significant
    + linkage scores. The Bootstrap Test estimates the precision of the QTL + location.
    +
    + +
    + + + + + + + + +
    + + + + + + + + + + + + + + + + + + +
    Display LRS greater than:
    Display all LRS
    Use Parents
    Use Weighted

    +
    +
    +
    Marker regression computes and displays LRS + values for individual markers.
    + This function also lists additive effects (phenotype units per allele) and
    + dominance deviations for some datasets.

    +
    + +
    + + + + + + + + +
    + + + + + + + + + + + + + + + + + + +
    Chromosome:
    Mapping Scale:
    Control Locus:

    + Permutation Test (n=2000)
    + Bootstrap Test (n=2000)
    + Use Parents
    +
    +
    +
    +
    Composite Interval Mapping allows you to control + for a single marker as
    + a cofactor. To find a control marker, run the Marker Regression function.
    +
    + +
    + + + + + + + + +
    + + + + + + + + + + + + +
    Sort by:
    Return:

    + Permutation Test + (n=500)
    +
    +
    +
    +
    Pair-Scan searches for pairs of chromosomal regions + that are
    + involved in two-locus epistatic interactions.
    +
    +
    +
    + +

      Review and Edit Data

    + + + +

    -
    + + - -
    +
    +
    +
    + Block samples +

    Edit or delete values in the Trait Data boxes, and use the + Reset option as + needed. +

    + + +
    + + + + +

    - Permutation Test - (n=500)
    + + + + +
    -
    + + {% if sample_groups[0].attributes %} +
    + + + + +
    + {% endif %}
    -
    Pair-Scan searches for pairs of chromosomal regions - that are
    - involved in two-locus epistatic interactions.
    -
    -
    -
    - -

      Review and Edit Data

    - - - -

    - -
    - - - -
    -
    -
    -
    - Block samples -

    Edit or delete values in the Trait Data boxes, and use the - Reset option as - needed. -

    - - -
    - - - - - - +
    + + + + + + + +
    +
    +
    +
    +

    Outliers highlighted in + yellow + can be hidden using + the Hide Outliers button. +

    + +

    Samples with no value (x) can be hidden by clicking + Hide No Value button. +

    - -
    - {% if sample_groups[0].attributes %} -
    - - + + + + + + + {% if sample_type.se_exists() %} + + + + {% endif %} + + {% for attribute in sample_type.attributes|sort() %} + + {% endfor %} + + + {% for sample in sample_type.sample_list %} + + + + + + {# Todo: Add IDs #} + + + {% if sample_type.se_exists() %} + + + {# Todo: Add IDs #} + + {% endif %} + + {# Loop through each attribute type and input value #} + {% for attribute in sample_type.attributes|sort() %} + {% endfor %} - - - + + {% endfor %} + +
    IndexSampleValue SE + {{ sample_type.attributes[attribute].name }} +
    + {{ loop.index }} + + + + {{ sample.name }} + + + + + ± + + + + {{ sample.extra_attributes[sample_type.attributes[attribute].name] }} +
    +
    - {% endif %} -
    -
    - - - - - - - -
    - -
    -
    -

    Outliers highlighted in - yellow - can be hidden using - the Hide Outliers button. -

    - -

    Samples with no value (x) can be hidden by clicking - Hide No Value button. -

    -
    -
    -
    - - - -
    - {% for sample_type in sample_groups %} -
    -

    {{ sample_type.header }}

    - -
    - - - - - - - - {% if sample_type.se_exists() %} - - - - {% endif %} - - {% for attribute in sample_type.attributes|sort() %} - - {% endfor %} - - - {% for sample in sample_type.sample_list %} - - - - - - {# Todo: Add IDs #} - - - {% if sample_type.se_exists() %} - - - {# Todo: Add IDs #} - - {% endif %} - - {# Loop through each attribute type and input value #} - {% for attribute in sample_type.attributes|sort() %} - - {% endfor %} - {% endfor %} - -
    IndexSampleValue SE - {{ sample_type.attributes[attribute].name }} -
    - {{ loop.index }} - - - - {{ sample.name }} - - - - - ± - - - - {{ sample.extra_attributes[sample_type.attributes[attribute].name] }} -
    -
    -
    - {% endfor %} -
    - -
    - - - - - - - - + + + + + + + + + + + + + @@ -1382,16 +1428,16 @@ --> - + - + - - - - - {% endblock %} + + + + +{% endblock %} -- cgit v1.2.3