Question: How to add search functions and additional fields to the html file of DESeq2 results created with ReportingTools
1
gravatar for da.de
4.2 years ago by
da.de10
Austria
da.de10 wrote:

Hi,

I started using the ReportingTools Package to visualize DESeq2 results including a ggplot2 graph, links and metadata. I really like the resulting html report.

However, I am looking for a way how to add some features:

  1. Automatically there is a filter option for numeric columns in the html report. How can I also add a search field to character columns (eg „gene symbol“)?
    There is only a general  „search all columns“ field which is in my case not very useful because I also have gene symbols in some metadata columns as well.
  2. How can I add a subtitle?
  3. Is it possible to add text fields (eg for experiment descriptions)?

Thanks for your help!

Best, Dagmar

 

 

#loop for making the pictures

imagename <- c()

for (i in 1:nrow(res_filtered))

{

  imagename[i]<- paste0("plot_", res_filtered $symbol[i], ".png")

  png(filename=paste0("reports/", imagename[i]))

  data <- plotCounts(dds, gene= res_filtered$ensembl[i], intgroup="Combined", returnData=TRUE)

  gp <- ggplot (data, aes(x=Combined, y=count))+

    geom_boxplot(fill="white", outlier.colour=NA)+

    geom_jitter(shape=16, size=4, aes(colour=Condition), position=position_jitter(width=0.2))

  print(gp)

  dev.off() 

}

#adding pictures + links to the data frame

my.df <- as.data.frame(res_filtered)

my.df$image <- hwriteImage(imagename, link=imagename, table=FALSE, width=100, height=100)

my.df$link <- hwrite(as.character(my.df$symbol), link=paste("http://www.ncbi.nlm.nih.gov/gene/",

                                                            as.character(my.df$entrez), sep=""), table=FALSE)

htmlreport5 <- HTMLReport (shortName="DEG_1",

                           title="DEG",

                           reportDirectory="./reports")

publish(my.df, htmlreport5)

finish(htmlreport5)

 

reportingtools deseq2 hwriter • 527 views
ADD COMMENTlink modified 4.2 years ago by James W. MacDonald51k • written 4.2 years ago by da.de10
Answer: How to add search functions and additional fields to the html file of DESeq2 res
0
gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald51k wrote:

1.) This is handled by the java scripts that come with the ReportingTools package. Every time you make an HTML table, there is a directory called jslib that is dropped in the same directory as your table. In there is a file called jsquery.dataTables.columnFilter.js, which seems to be in charge of doing the filtering, so I would start there.

2.) Not sure what you mean by subtitle. Subtitle to what? But do note that most of the basic HTML is handled by the hwriter package, and there is an extensive set of examples, showing how to do any number of things, so I would start there.

3.) See #2

ADD COMMENTlink written 4.2 years ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 148 users visited in the last hour