Nozzle Demo Report 1
Maintained by Nils Gehlenborg (Harvard Medical School)
Overview
Introduction

Nozzle is an R Package to generate reports for high-throughput data analysis pipelines based on HTML, CSS and JavaScript. However, to use Nozzle, no knowledge of these technologies is required.

Summary

A simple API that enables developers to design efficient reports quickly.

Results
Nozzle Figure

Figure 1.  Get High-res Image An example for a figure. Everything that is shown in the figure should be explained in the caption. The figure needs to have axis labels and a legend.

Figure 2.  An example for a figure without a link to a high-res file.

Nozzle Table

Table 1.  Get Full Table A small table. All parameters shown in the columns of the table need to be explained in the caption.

Composite.Element.REF p difference q subclass
CREB3L1 0.0001831334 -0.1728373 0.00009707283 1
PNMA1 3.106446e-07 0.2215378 2.615609e-07 1
MMP2 2.409105e-19 -1.089666 1.349472e-18 1
SMARCD3 0.0002684664 -0.3087688 0.0001376014 1
A4GNT 0.0003266416 0.0830912 0.0001643772 1
C9ORF39 0.006297307 0.1699754 0.002475277 1
PKNOX2 0.02737617 0.1164925 0.009354365 1
RALYL 0.00003812137 0.1484151 0.00002279739 1
ZHX3 0.001407828 0.09064685 0.0006314806 1
RXFP3 1.891887e-07 0.1587289 1.645746e-07 1

Table 2.  Get Full Table A small table without content but a link to the full table.

Composite.Element.REF p difference q subclass
Get Full Table

Table 3.  A small table without a link to a file. The values in this table have been trimmed to 2 significant digits.

Composite.Element.REF p difference q subclass
CREB3L1 0.00018 -0.17 0.000097 1
PNMA1 3.1e-07 0.22 2.6e-07 1
MMP2 2.4e-19 -1.1 1.3e-18 1
SMARCD3 0.00027 -0.31 0.00014 1
A4GNT 0.00033 0.083 0.00016 1
C9ORF39 0.0063 0.17 0.0025 1
PKNOX2 0.027 0.12 0.0094 1
RALYL 0.000038 0.15 0.000023 1
ZHX3 0.0014 0.091 0.00063 1
RXFP3 1.9e-07 0.16 1.6e-07 1

Table 4.  Get Full Table A long table (GISTIC 2 output). The values in this table have been trimmed to 2 significant digits.

Type Chromosome Start End X.log10.q.value. G.score average.amplitude frequency
Amp 1 772112 894470 0 0.015 0.53 0.08
Amp 1 908436 980702 0 0.011 0.53 0.078
Amp 1 993492 1176318 0 0.014 0.53 0.08
Amp 1 1176340 1491459 0 0.017 0.54 0.084
Amp 1 1494604 1495961 0 0.02 0.54 0.087
Amp 1 1677547 1699248 0 0.021 0.56 0.084
Amp 1 1701274 1781662 0 0.015 0.55 0.08
Amp 1 1783646 2179440 0 0.012 0.55 0.078
Amp 1 2180264 2325377 0 0.016 0.58 0.078
Amp 1 2342140 2544147 0 0.014 0.56 0.076
Amp 1 2558317 2569201 0 0.02 0.58 0.078
Amp 1 2684305 2691676 0 0.043 0.68 0.08
Amp 1 2694496 2836134 0 0.039 0.64 0.08
Amp 1 2836836 2869403 0 0.015 0.54 0.076
Amp 1 2893916 3113601 0 0.019 0.55 0.078
Amp 1 3114015 3466139 0 0.018 0.55 0.076
Amp 1 3470009 3545641 0 0.014 0.54 0.074
Amp 1 3548122 4786628 0 0.0081 0.53 0.071
Amp 1 4787247 5039596 0 0.012 0.54 0.069
Amp 1 5040086 5247299 0 0.0081 0.53 0.067
Amp 1 5252352 5290438 0 0.013 0.55 0.069
Amp 1 5290540 6461908 0 0.0081 0.53 0.067
Amp 1 6463727 6464917 0 0.013 0.55 0.069
Amp 1 6470257 6525533 0 0.016 0.55 0.071
Amp 1 6529195 6611445 0 0.02 0.56 0.074
Amp 1 6612727 6622404 0 0.017 0.56 0.071
Amp 1 6627943 6753649 0 0.013 0.55 0.069
Amp 1 6756933 7748980 0 0.0081 0.54 0.067
Amp 1 7751694 7866851 0 0.017 0.58 0.069
Amp 1 7869860 8370779 0 0.0081 0.54 0.067
Amp 1 8372593 8470467 0 0.018 0.59 0.069
Amp 1 8478621 8684617 0 0.0081 0.54 0.069
Amp 1 8684638 8753870 0 0.013 0.55 0.074
Amp 1 8755086 8813381 0 0.015 0.55 0.076
Amp 1 8813395 9081584 0 0.013 0.55 0.074
Amp 1 9081699 9327567 0 0.0081 0.54 0.071
Amp 1 9329566 9606408 0 0.014 0.56 0.074
Amp 1 9618451 9661466 0 0.046 0.71 0.076
Amp 1 9665572 9723928 0 0.05 0.71 0.078
Amp 1 9726173 9775286 0 0.046 0.71 0.076
Amp 1 9778175 9803699 0 0.051 0.74 0.076
Amp 1 9813558 9819349 0 0.019 0.59 0.074
Amp 1 9819588 10090534 0 0.014 0.56 0.074
Amp 1 10094018 10155121 0 0.019 0.57 0.076
Amp 1 10158626 10226824 0 0.024 0.58 0.078
Amp 1 10230040 10264177 0 0.019 0.57 0.076
Amp 1 10264582 10279993 0 0.024 0.6 0.076
Amp 1 10280179 10512423 0 0.019 0.57 0.076
Amp 1 10513691 10846150 0 0.014 0.56 0.074
Amp 1 10851596 10925166 0 0.047 0.71 0.078
Amp 1 10929659 11231990 0 0.041 0.69 0.076
Amp 1 11237699 11266331 0 0.066 0.8 0.08
Amp 1 11270079 11287507 0 0.041 0.68 0.08
Amp 1 11297646 11421975 0 0.062 0.77 0.082
Amp 1 11425416 11604155 0 0.041 0.68 0.08
Amp 1 11607087 11706705 0 0.065 0.78 0.082
Amp 1 11706775 11733431 0.031 0.068 0.78 0.084
Amp 1 11737218 11755449 0 0.059 0.73 0.084
Amp 1 11757041 11777258 0 0.065 0.74 0.087
Amp 1 11783111 11804503 0.094 0.071 0.77 0.087
Amp 1 11806238 11819532 0 0.065 0.76 0.084
Amp 1 11820345 11852155 0 0.063 0.77 0.082
Amp 1 11855728 11882256 0.049 0.069 0.78 0.084
Amp 1 11882981 11899219 0 0.063 0.77 0.082
Amp 1 11899545 12031882 0.0076 0.067 0.77 0.084
Amp 1 12035827 12164488 0 0.063 0.77 0.082
Amp 1 12170878 12343606 0 0.041 0.68 0.08
Amp 1 12348657 12397325 0 0.063 0.78 0.082
Amp 1 12404846 12432898 0 0.066 0.77 0.084
Amp 1 12433864 12472284 0 0.043 0.68 0.082
Amp 1 12474856 12759029 0 0.041 0.68 0.08
Amp 1 13415688 13700026 1.1 0.11 0.98 0.08
Amp 1 13707597 13735337 1.6 0.12 1 0.082
Amp 1 13744529 14000739 2.7 0.15 1.2 0.084
Amp 1 14001413 14049337 3.4 0.17 1.2 0.087
Amp 1 14052740 14080664 3.7 0.18 1.2 0.087
Amp 1 14082273 14174021 3.3 0.17 1.2 0.087
Amp 1 14174311 14183961 3.6 0.18 1.2 0.087
Amp 1 14245743 14249606 2.4 0.14 1.1 0.084
Amp 1 14250501 14264038 2 0.13 1.1 0.084
Amp 1 14270390 14307445 1.5 0.12 1 0.082
Amp 1 14311796 14440278 1.1 0.11 0.99 0.08
Amp 1 14443436 14571802 0.17 0.073 0.85 0.078
Amp 1 14574277 14629827 0.71 0.094 0.92 0.08
Amp 1 14632085 14965634 0.17 0.073 0.85 0.078
Amp 1 14968809 14987081 0.81 0.098 0.94 0.08
Amp 1 14988097 15075316 0.17 0.073 0.85 0.078
Amp 1 15075844 15086416 0.23 0.076 0.84 0.08
Amp 1 15096416 15178638 0 0.043 0.7 0.078
Amp 1 15180065 15206335 0 0.062 0.77 0.08
Amp 1 15208446 15235131 0 0.057 0.75 0.08
Amp 1 15238827 15349038 0 0.043 0.7 0.078
Amp 1 15349533 15350653 0 0.046 0.7 0.08
Amp 1 15351396 15379907 0 0.05 0.7 0.082
Amp 1 15380370 15469445 0 0.055 0.71 0.084
Amp 1 15472394 15505176 0 0.058 0.7 0.087
Amp 1 15509309 15520415 0 0.054 0.7 0.084
Amp 1 15526432 15572014 0.23 0.076 0.78 0.087
Amp 1 15573004 15577894 0 0.043 0.65 0.084
Amp 1 15578770 15833195 0 0.021 0.56 0.082
Nozzle Text

Nozzle supports a range of different formatting styles: strong; emph; parameter = value; filename; code;

  • Nozzle also provides lists.

  • They can even be nested.

    1. They may contain other lists.

    2. Or selected other elements.

    3. Numbered.

  • Or unnumbered.

The Nozzle package [1] also supports referencing of figures, tables and references [2][3] that are part of the report. For instance, developers can refer to a figure1, such as Figure 1, or to a table, such as Table 1.

Nozzle reports may also contain results with different levels of protection. For instance, this paragraph is labeled 'PUBLIC' and will be included in all reports. However, the next paragraph is labeled 'GROUP' and will only be included in reports for members of the TCGA Consortium. The paragraph after the next is even more restricted and labeled 'PRIVATE', which means that it will only show up in internal reports. Please note that if you are viewing the public version or the TCGA/group version of the report you might not see any paragraphs or only one paragraph after this one.

This paragraph is protected and will only be included in reports for members of the TCGA Consortium.

This is a private paragraph. Hardly anyone gets to see this.

Nozzle Results
Subsubsection!

Text in a subsubsection! But the next paragraph belongs to the "Nozzle Results" subsection.

A particularly fun aspect of Nozzle is how it handles results and summaries of results. For instance, we have found that A = 53030, which is totally an amazing result. It is not significant.

My Rocking Result
My Rocking Subresult
My Subrocking Subresult

This is a paragraph related to the rocking result of A = 53030. Results may contain all sorts of section, figures, tables, list and so on. But no more results, please!

  • This is another list.

  • It contains a result: B = 1234

    • My Rocking Result

    This is a paragraph related to the rocking result of A = 53030. Results may contain all sorts of section, figures, tables, list and so on. But no more results, please!

    Figure S2.  Get High-res Image Anothr pictur from Flickr.

    Table S1.  Get Full Table A long table (GISTIC 2 output). The values in this table have been trimmed to 2 significant digits.

    Type Chromosome Start End X.log10.q.value. G.score average.amplitude frequency
    Amp 1 772112 894470 0 0.015 0.53 0.08
    Amp 1 908436 980702 0 0.011 0.53 0.078
    Amp 1 993492 1176318 0 0.014 0.53 0.08
    Amp 1 1176340 1491459 0 0.017 0.54 0.084
    Amp 1 1494604 1495961 0 0.02 0.54 0.087
    Amp 1 1677547 1699248 0 0.021 0.56 0.084
    Amp 1 1701274 1781662 0 0.015 0.55 0.08
    Amp 1 1783646 2179440 0 0.012 0.55 0.078
    Amp 1 2180264 2325377 0 0.016 0.58 0.078
    Amp 1 2342140 2544147 0 0.014 0.56 0.076
    Amp 1 2558317 2569201 0 0.02 0.58 0.078
    Amp 1 2684305 2691676 0 0.043 0.68 0.08
    Amp 1 2694496 2836134 0 0.039 0.64 0.08
    Amp 1 2836836 2869403 0 0.015 0.54 0.076
    Amp 1 2893916 3113601 0 0.019 0.55 0.078
    Amp 1 3114015 3466139 0 0.018 0.55 0.076
    Amp 1 3470009 3545641 0 0.014 0.54 0.074
    Amp 1 3548122 4786628 0 0.0081 0.53 0.071
    Amp 1 4787247 5039596 0 0.012 0.54 0.069
    Amp 1 5040086 5247299 0 0.0081 0.53 0.067
    Amp 1 5252352 5290438 0 0.013 0.55 0.069
    Amp 1 5290540 6461908 0 0.0081 0.53 0.067
    Amp 1 6463727 6464917 0 0.013 0.55 0.069
    Amp 1 6470257 6525533 0 0.016 0.55 0.071
    Amp 1 6529195 6611445 0 0.02 0.56 0.074
    Amp 1 6612727 6622404 0 0.017 0.56 0.071
    Amp 1 6627943 6753649 0 0.013 0.55 0.069
    Amp 1 6756933 7748980 0 0.0081 0.54 0.067
    Amp 1 7751694 7866851 0 0.017 0.58 0.069
    Amp 1 7869860 8370779 0 0.0081 0.54 0.067
    Amp 1 8372593 8470467 0 0.018 0.59 0.069
    Amp 1 8478621 8684617 0 0.0081 0.54 0.069
    Amp 1 8684638 8753870 0 0.013 0.55 0.074
    Amp 1 8755086 8813381 0 0.015 0.55 0.076
    Amp 1 8813395 9081584 0 0.013 0.55 0.074
    Amp 1 9081699 9327567 0 0.0081 0.54 0.071
    Amp 1 9329566 9606408 0 0.014 0.56 0.074
    Amp 1 9618451 9661466 0 0.046 0.71 0.076
    Amp 1 9665572 9723928 0 0.05 0.71 0.078
    Amp 1 9726173 9775286 0 0.046 0.71 0.076
    Amp 1 9778175 9803699 0 0.051 0.74 0.076
    Amp 1 9813558 9819349 0 0.019 0.59 0.074
    Amp 1 9819588 10090534 0 0.014 0.56 0.074
    Amp 1 10094018 10155121 0 0.019 0.57 0.076
    Amp 1 10158626 10226824 0 0.024 0.58 0.078
    Amp 1 10230040 10264177 0 0.019 0.57 0.076
    Amp 1 10264582 10279993 0 0.024 0.6 0.076
    Amp 1 10280179 10512423 0 0.019 0.57 0.076
    Amp 1 10513691 10846150 0 0.014 0.56 0.074
    Amp 1 10851596 10925166 0 0.047 0.71 0.078
    Amp 1 10929659 11231990 0 0.041 0.69 0.076
    Amp 1 11237699 11266331 0 0.066 0.8 0.08
    Amp 1 11270079 11287507 0 0.041 0.68 0.08
    Amp 1 11297646 11421975 0 0.062 0.77 0.082
    Amp 1 11425416 11604155 0 0.041 0.68 0.08
    Amp 1 11607087 11706705 0 0.065 0.78 0.082
    Amp 1 11706775 11733431 0.031 0.068 0.78 0.084
    Amp 1 11737218 11755449 0 0.059 0.73 0.084
    Amp 1 11757041 11777258 0 0.065 0.74 0.087
    Amp 1 11783111 11804503 0.094 0.071 0.77 0.087
    Amp 1 11806238 11819532 0 0.065 0.76 0.084
    Amp 1 11820345 11852155 0 0.063 0.77 0.082
    Amp 1 11855728 11882256 0.049 0.069 0.78 0.084
    Amp 1 11882981 11899219 0 0.063 0.77 0.082
    Amp 1 11899545 12031882 0.0076 0.067 0.77 0.084
    Amp 1 12035827 12164488 0 0.063 0.77 0.082
    Amp 1 12170878 12343606 0 0.041 0.68 0.08
    Amp 1 12348657 12397325 0 0.063 0.78 0.082
    Amp 1 12404846 12432898 0 0.066 0.77 0.084
    Amp 1 12433864 12472284 0 0.043 0.68 0.082
    Amp 1 12474856 12759029 0 0.041 0.68 0.08
    Amp 1 13415688 13700026 1.1 0.11 0.98 0.08
    Amp 1 13707597 13735337 1.6 0.12 1 0.082
    Amp 1 13744529 14000739 2.7 0.15 1.2 0.084
    Amp 1 14001413 14049337 3.4 0.17 1.2 0.087
    Amp 1 14052740 14080664 3.7 0.18 1.2 0.087
    Amp 1 14082273 14174021 3.3 0.17 1.2 0.087
    Amp 1 14174311 14183961 3.6 0.18 1.2 0.087
    Amp 1 14245743 14249606 2.4 0.14 1.1 0.084
    Amp 1 14250501 14264038 2 0.13 1.1 0.084
    Amp 1 14270390 14307445 1.5 0.12 1 0.082
    Amp 1 14311796 14440278 1.1 0.11 0.99 0.08
    Amp 1 14443436 14571802 0.17 0.073 0.85 0.078
    Amp 1 14574277 14629827 0.71 0.094 0.92 0.08
    Amp 1 14632085 14965634 0.17 0.073 0.85 0.078
    Amp 1 14968809 14987081 0.81 0.098 0.94 0.08
    Amp 1 14988097 15075316 0.17 0.073 0.85 0.078
    Amp 1 15075844 15086416 0.23 0.076 0.84 0.08
    Amp 1 15096416 15178638 0 0.043 0.7 0.078
    Amp 1 15180065 15206335 0 0.062 0.77 0.08
    Amp 1 15208446 15235131 0 0.057 0.75 0.08
    Amp 1 15238827 15349038 0 0.043 0.7 0.078
    Amp 1 15349533 15350653 0 0.046 0.7 0.08
    Amp 1 15351396 15379907 0 0.05 0.7 0.082
    Amp 1 15380370 15469445 0 0.055 0.71 0.084
    Amp 1 15472394 15505176 0 0.058 0.7 0.087
    Amp 1 15509309 15520415 0 0.054 0.7 0.084
    Amp 1 15526432 15572014 0.23 0.076 0.78 0.087
    Amp 1 15573004 15577894 0 0.043 0.65 0.084
    Amp 1 15578770 15833195 0 0.021 0.56 0.082

  • And an empty result: C = Oh no!

  • That's nice!

Table 5.  Get Full Table Another small table. This table has result1 summaries associated with it. All parameters shown in the columns of the table need to be explained in the caption.

Composite.Element.REF p difference q subclass
CREB3L1 0.00018 -0.17 0.000097 1
PNMA1 3.1e-07 0.22 2.6e-07 1
MMP2 2.4e-19 -1.1 1.3e-18 1
SMARCD3 0.00027 -0.31 0.00014 1
A4GNT 0.00033 0.083 0.00016 1
C9ORF39 0.0063 0.17 0.0025 1
PKNOX2 0.027 0.12 0.0094 1
RALYL 0.000038 0.15 0.000023 1
ZHX3 0.0014 0.091 0.00063 1
RXFP3 1.9e-07 0.16 1.6e-07 1
Result 2

This is a paragraph related to PNMA1.

Result 4

This is a paragraph related to SMARCD3.

Result 6

This is a paragraph related to C9ORF39.

Result 8

This is a paragraph related to RALYL.

Result 10

This is a paragraph related to RXFP3.

Methods & Data
Input

This section should list the files that were used as input.

  • methylation file = /path/to/this/great/file

  • gene expression file = /path/to/gene/expression/file

Really Cool Method

A typical method description consists of one or two paragraphs of text describing the method, followed by a list of method parameters and their values for the present run.

  • param alpha = Bet

  • param beta = Carotene

  • param gamma = rays

Pretty Fast Method

A typical method description consists of one or two paragraphs of text describing the method, followed by a list of method parameters and their values for the present run.

  • n = x

  • Q = 1034

  • T = 4.4

References
[1] Nils Gehlenborg, The Nozzle Report Package (2011)
[3] Nils Gehlenborg, Nozzle: An R Package for Report Generation, Yet Another Bioinformatics Journal 14(44):783-789 (2011)