• create addInteractive( ... ) for general javascript based views within a div
• create addGraph()
• use case: workflow DAG
• details: https://github.com/trifacta/vega

e.g. to be used to insert user-defined HTML into a div

For instance to link to the report for the same analysis applied to different inputs.

Check test for logo inclusion. This seems to be broken.

If using English coding or Unicode in the browser, Chinese characters failed to show correctly.

When using Chinese character coding, namely GBK, Nozzle report will collapse to a narrow window that couldn't be viewed properly. But, If maximize the browser window, the problem is gone.

Hi,
Is it possible to support the DT (https://rstudio.github.io/DT/) for table visualization in nozzle framework?
Best regards!
Bo

See Mike's suggestion:

http://gdac.broadinstitute.org/runs/tmp/expand.html

This

should fold out into this

It would be nice if the reference (i.e. "[#]") was a link that navigates to the associated reference in the references section of the report.

Right now it is not obvious that they can be clicked for sorting.

Hi,

It would be nice if Nozzle was able to support languages other than English, such as Mandarin Chinese.

Thank you!

should be referring to the Bioinformatics publication

the corresponding R script:
setwd('C:/Users/Lenovo/Desktop')

require( "Nozzle.R1" );
#分析方法
r <- newCustomReport( "My Report" );
s1<- newSection('分析方法')

#########
r<- addTo(r,s1)
writeReport(r,filename = 'reports/my_report',credits = FALSE)
neither html nor browser can correctly show Chinese charater.

my_report.html.txt

Numerical columns should be right aligned by default (easier to read) and all others should be left or center aligned (as defined by the report author).

• subtitle style
• concatenate with title for page title, etc.

Like here:

http://gdac.broadinstitute.org/runs/tmp/expand.html

Problems:

• not same as generation date
• not same date as aggregation date

I've been seeing the following issue using Chrome 23.0.1271.97 (http://gdac.broadinstitute.org/runs/awg_hnsc__2013_03_30/reports/cancer/HNSC-TP-ALL/copynumber/gistic2/nozzle.html).

In order to link to sections, figures, tables we would like to define anchors for these elements when their corresponding "newXXX" method is called.

In a perfect world, the "writeReport" method would generate a warning if duplicate anchors exist.

• DOI should be included in a "How to Cite?" section.
• a resolver URL should be provided.
• generate warning/error if a DOI is set and user tries to set another DOI?

This should be below the title and above the first section.

It would be really nice if newCitation() had a DOI field, which would cause the citation to link to http://dx.doi.org/,as well as properly place the DOI in the citation.

The same approach that is used to connect the content of a table cell to supplementary information could be used.

Sorry to bother, and maybe you're already aware of this, but the W3C validation service points out many
concerns for the Nozzle reports. For example, when giving it this URL

http://gdac.broadinstitute.org/runs/analyses__2013_03_26/reports/cancer/OV/index.html

and specifying HTML5 (experimental) validation, I get 27 issues reported. If I instead ask it to validate
against HTML4 transitional, it yields an order of magnitude more.

Just FYI,
Mike

There appears to be a small bug, presumably in the javascript, which means that alphanumeric columns in tables cannot be sorted when using Nozzle. Here is a small test example.

library("Nozzle.r1")
num = c(1,2,3,2.1)
txt <- c("aada","aaba", "aaca","aaaa")
alphanum <- c("aad1", "aab2", "aac3", "aaa4")
d <- data.frame(numeric=num, text=txt, alphanumeric=alphanum)
report <- newCustomReport("Alphanumeric sorting test")
t <- newTable(d, "Test table")
report <- addTo(report, t)
writeReport(report, "test")

In the html output, it is possible to sort the "numeric" and "text" columns, but the "alphanumeric" column does not sort correctly.

Any insight gratefully received.

I found the bug in nozzle report.

In fact, this situation I already reported to Nils, but I can't found the solution in those days.

After about 2 year, finally I found the cause of problem. (guess)

please check this problem

setting a default encoding within the HTML of the report

It would be extremely useful if the following flags were added to new{Section,SubSection,SubSubSection}:

• collapsable
  • indicate if a Section/SubSection/SubSubSection is collapsable
• collapsed
  • indicate if a Section/SubSection/SubSubSection begins collapsed (if collapsable is FALSE, this would be force-set to FALSE regardless of user seting)

In cases where a subsection is included in a subsection indentation would help to tell different levels of the hierarchy apart.

The check for the presence of the subtitle attribute is not working properly.

Currently, the user needs to click on a figure in order to enlarge it. It would be good one could specify expanded=TRUE in newFigure, so that they are enlarged by default.