ReportingTools: an automated
result processing toolkit for high
throughput genomic analyses
Jessica Larson, PhD
Computational Biologist
Genentech, Inc.
larson.jessica@gene.com
July 19 2013
© 2013, Genentech
Outline
(1)
(2)
(3)
(4)
(5)
ReportingTools introduction and basics
ReportingTools and microarray experiments
ReportingTools and RNA-seq experiments
ReportingTools and knitr
ReportingTools and shiny
1
ReportingTools
Genomic analyses output
Microarray
Next-gen
Sequence
Geneset
Tabular Data
GO: 0016581
G O: 0000118GO: 0005667G O: 0016592GO: 0017053
G O: 0090545
G O: 0034707
G O: 0044451
G O: 0034702 GO: 0032587
G O: 0030690GO: 0042613
G O: 0042612
G O: 0001726GO: 0031256
G O: 0030686GO: 0030687
G O: 0009897GO: 0070436
G O: 0071062
Assay data
G O: 0031252
GO: 0042611
GO: 0030684
GO: 0016323
G O: 0031264
G O: 0044459
G O: 0031265
G O: 0008287G O: 0035693
G O: 0035692G O: 0070022
G O: 0008305
G O: 0005654
G O: 0031226 GO: 0016324
GO: 0043234
GO: 0071556
G O: 0043235
GO: 0031224
GO: 0030426
G O: 0044306
G O: 0071565
G O: 0000159G O: 0005887GO: 0070032
G O: 0070044
G O: 0033256
G O: 0000307G O: 0030689
G O: 0016021GO: 0031225
G O: 0031201
GO: 0031526
G O: 0031253
GO: 0032991
G O: 0005886G O: 0044425
G O: 0043025
GO: 0044297
G O: 0030427
G O: 0071564
GO: 0043197
G O: 0043005
G O: 0005929
GO: 0005902
G O: 0044463G O: 0030529
G O: 0031143GO: 0030175
G O: 0005903
G O: 0097458
G O: 0042995
G O: 0030018
G O: 0090544 G O: 0016514GO: 0071778
GO: 0014069
G O: 0031514GO: 0072372
G O: 0044327
G O: 0030424G O: 0030425 GO: 0044309
GO: 0009986
G O: 0042622
G O: 0031528 GO: 0008250
G O: 0001750
G O: 0044441 GO: 0031513
GO: 0005905
G O: 0045121
G O: 0071944
G O: 0031674
GO: 0070603
G O: 0030017
G O: 0044432
GO: 0005840
G O: 0048471
GO: 0005829G O: 0043292GO: 0048786
GO: 0030176
GO: 0001931
GO: 0005741
GO: 0031301G O: 0031227
G O: 0031968G O: 0005764
G O: 0044440GO: 0005769
GO: 0005637
G O: 0005766 G O: 0005765G O: 0043202GO: 0031966
GO: 0000139
G O: 0031300 GO: 0005774
G O: 0005775
GO: 0000323
G O: 0005783GO: 0032421
G O: 0016020
G O: 0005768
G O: 0019867
G O: 0044444
GO: 0005622
GO: 0012505G O: 0005773GO: 0031090
G O: 0042582
G O: 0005758G O: 0031965
G O: 0005641
G O: 0005740G O: 0005635GO: 0019866
G O: 0031970
GO: 0044429
G O: 0044431
G O: 0005739
G O: 0031967
G O: 0005794G O: 0044446GO: 0005938
GO: 0031094
GO: 0043231
GO: 0030670
G O: 0000775G O: 0000785G O: 0044454
G O: 0030864
G O: 0030863
G O: 0005802
G O: 0016363
G O: 0044427G O: 0000793G O: 0000228
GO: 0008290
G O: 0042641
G O: 0031095GO: 0032588
G O: 0043227
GO: 0044424
GO: 0043209
G O: 0044437
G O: 0044422
GO: 0005737
G O: 0031254
G O: 0045177
GO: 0005640
G O: 0005771G O: 0031902
G O: 0031901
G O: 0005789 GO: 0005770
G O: 0010008
GO: 0042175G O: 0030016GO: 0032420
G O: 0044449
G O: 0000790
G O: 0005874GO: 0005694
G O: 0044428G O: 0070013
G O: 0044448G O: 0045120
G O: 0034399
G O: 0031981
GO: 0031974
GO: 0043229
G O: 0043228
G O: 0043226
G O: 0031975
G O: 0044464
G O: 0005623
G O: 0005813
G O: 0030658G O: 0030134
GO: 0005819
G O: 0005815G O: 0005798
G O: 0030662
G O: 0031088G O: 0031092
G O: 0008021G O: 0031093
G O: 0030139 GO: 0030136
G O: 0042827G O: 0030667
G O: 0042581 G O: 0031091GO: 0034774
G O: 0042470
GO: 0030133
G O: 0030659GO: 0030135
G O: 0030141G O: 0060205
G O: 0048770
G O: 0012506GO: 0044433
G O: 0016023G O: 0031983
G O: 0070062G O: 0045211
G O: 0005856
GO: 0043232
G O: 0030672
G O: 0012507G O: 0045335G O: 0030666GO: 0030665 G O: 0045334
G O: 0005730
G O: 0015629GO: 0044430
G O: 0015630 GO: 0045111
G O: 0005634GO: 0043233
G O: 0005801
GO: 0030669
G O: 0031410G O: 0031988
G O: 0097060
G O: 0031982G O: 0065010G O: 0044456GO: 0031594
G O: 0043230
G O: 0005604
G O: 0072563
G O: 0072562
G O: 0044420
G O: 0005578
G O: 0005615
G O: 0031012
G O: 0044421
GO: 0005576
G O: 0045202
G O: 0005916
G O: 0005925
G O: 0014704GO: 0005913
G O: 0005924
G O: 0005921 G O: 0044291
G O: 0005912
G O: 0005911 GO: 0070161GO: 0030055
G O: 0030054
G O: 0005575
Bioconductor
analysis tool
limma
DESeq
DESeq2
edgeR
DEXSeq
GOStats
GSEAlm
PFAM
data.frame
ReportingTools: analysis processing and presentation
Automated processes
Result detection
detection of analysis type
object-oriented dispatching
requires only 3 lines of code
Result preparation
analysis -specific
modular and customizable
cross-link to
public databases
analysis-specific
graphics
additional
annotations
Result presentation
search, filter, and sort
functionality added by
default flexible css styling
2
Example output and code from the package
vignettes
http://research-pub.gene.com/ReportingTools/
3
Publishing a data.frame
There are three basic calls to publish to an HTML page:
(1) Define the report with
htmlRep <HTMLReport(shortName ='my_html_file',
reportDirectory = './reports’)
(2) Fill the report with
publish(iris, htmlRep)
(3) Close the report with
finish(htmlRep)
4
Publishing the Iris data
library(ReportingTools)
data(iris)
htmlRep <- HTMLReport(shortName = 'my_html_file',
reportDirectory = './reports')
publish(iris, htmlRep)
finish(htmlRep)
5
More basics with the Iris data
I.
Adding plots (including basic,
lattice, .png, .pdf)
II. Adding text (including links to
other pages)
III. Adding additional tables
IV. Modify data frames upon
publication (.modifyDF)
V. Publishing to CSV files
(CSVFile)
6
Using .modifyDF
htmlRep <- HTMLReport(shortName = 'my_html_file_modify',
title = 'Manipulating the data frame directly before
publishing’, reportDirectory = './reports')
publish(iris, htmlRep, numdigits = 1,
.modifyDF = list(roundLength, makeImages, addSpeciesLink, cleanUpDF))
finish(htmlRep)
7
Outline
(1)
(2)
(3)
(4)
(5)
ReportingTools introduction and basics
ReportingTools and microarray experiments
ReportingTools and RNA-seq experiments
ReportingTools and knitr
ReportingTools and shiny
8
Microarray examples
I. Publish output from limma (add new images
and links)
II. Publish GO and PFAM analysis output
III. Publish gene sets
IV. Create index pages
9
Outline
(1)
(2)
(3)
(4)
(5)
ReportingTools introduction and basics
ReportingTools and microarray experiments
ReportingTools and RNA-seq experiments
ReportingTools and knitr
ReportingTools and shiny
10
RNA-seq
Methods for:
I. edgeR exact tests
II. edgeR LRTs
III.DESeq
IV.DESeq2 (with .modifyDF and .toDF)
11
Outline
(1)
(2)
(3)
(4)
(5)
ReportingTools introduction and basics
ReportingTools and microarray experiments
ReportingTools and RNA-seq experiments
ReportingTools and knitr
ReportingTools and shiny
12
knitr
Can easily integrate ReporingTools tables into knitr reports
Need to call ‘knit2html’ from report directory and specify the knitrHandlers in
HTMLReport()
> setwd("reports")
> library(knitr)
> knit2html("/home/ubuntu/4BioCknitr.Rmd”)
13
Updates to run the knitr example (due to permission
issues)
(1)
(2)
(3)
(4)
Open 4BioCknitr.Rmd
Save to the /home/ubuntu directory
setwd(“reports”)
Then call knit2html("/home/ubuntu/4BioCknitr.Rmd")
14
Outline
(1)
(2)
(3)
(4)
(5)
ReportingTools introduction and basics
ReportingTools and microarray experiments
ReportingTools and RNA-seq experiments
ReportingTools and knitr
ReportingTools and shiny
15
Shiny and ReportingTools
16
Updates to run the shiny example (due to
permission issues)
(1)
(2)
(3)
(4)
Open server.R and ui.R
Save these to the /home/ubuntu/reports directory
setwd(“reports”)
Then call myRunApp()
17
Changes to server.R
(1) Create a report with shinyHandlers to stream the HTML form of any
elements added to our Report:
htmlrep <- HTMLReport(reportDirectory = "./", shortName="bigtest", handlers = shinyHandlers)
(2) Define a custom rendering function so that shiny can ‘hear’ elements
being added to our report and insert them into the dynamic HTML:
renderRepTools <- function(expr, env=parent.frame(), quoted=FALSE) {
func <- exprToFunction(expr, env, quoted)
function(){
paste(capture.output(func()), collapse="\n")
}
}
(3) Publish elements to our report within the expression passed to
renderRepTools:
output$view2 <- renderRepTools({
publish(datasetInput(), htmlrep)
})
18
Changes to ui.R
(1) Include the JavaScript and CSS files so that the ReportingTools tables
function properly via custHeaderPanel function:
##this function accepts the tile and window title arguments by shiny's headerpanel function
##plus the js and cs arguments
custHeaderPanel = function(title, windowTitle =title, js= NULL, css=NULL){
mytlist = c(lapply(js, function(x) tags$script(HTML(paste(readLines(x), collapse="\n")))),
lapply(css, function(x) tags$style(HTML(paste(readLines(x), collapse="\n")))))
tagList(tag("head",mytlist), div(class = "span12",
style = "padding: 10px 0px;", h1(title)))
}
# Define UI for dataset viewer application
shinyUI(pageWithSidebar(
custHeaderPanel("ReportingTools",
js = list.files(system.file("extdata/jslib", package="ReportingTools"),
full.names=TRUE),
css = list.files(system.file("extdata/csslib", package="ReportingTools"),
pattern="bootstrap.css", full.names=TRUE),
),
19
Changes to ui.R
(2) Declare elements formated by ReportingTools as htmlOutput
mainPanel(
verbatimTextOutput("summary"),
htmlOutput("view2")
)
This indicates to the shiny system that the output with be HTML code
20
Future methods
DESeq2 methods
Return the decorated DF
More flexibility with annotations
21
Acknowledgements
Jason Hackney
Josh Kaminker
Melanie Huntley
Christina Chaivorapol
Gabriel Becker
Michael Lawrence
Robert Gentleman
Martin Morgan
Dan Tenenbaum
22