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:
- 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. - How can I add a subtitle?
- 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)