I am learning about using ReportingTools for DESeqDataSet. Using the example in the user guide:
library(DESeq2) library(ReportingTools) data(mockRnaSeqData) conditions <- c(rep("case",3), rep("control", 3)) mockRna.dse <- DESeqDataSetFromMatrix(countData = mockRnaSeqData, colData = as.data.frame(conditions), design = ~ conditions) colData(mockRna.dse)$conditions <- factor(colData(mockRna.dse)$conditions, levels=c("control", "case")) # Get a DESeqDataSet object mockRna.dse <- DESeq(mockRna.dse) # Now the results can be written to a report using the DESeqDataSet object. des2Report <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2', title = 'RNA-seq analysis of differential expression using DESeq2', reportDirectory = "./reports") # COMMENT 1: I added n=100 so it doesn't take so long # COMMENT 2: .modifyDF = list(myFunc1, myFunc2) or .modifyDF = list() # makes the Images disappear from the HTML publish(mockRna.dse,des2Report, pvalueCutoff=0.05, n = 100, annotation.db="org.Mm.eg.db", factor = colData(mockRna.dse)$conditions, reportDir="./reports") url <- finish(des2Report) browseURL(url)
The HTML output has an Image column with stripplots of expression counts for each gene.
It is possible to write functions which modify the data frame, and
publish can call these functions if they are passed as a list via the
.modifyDF argument, e.g.
.modifyDF = list(myFunc1, myFunc2)
However, when I do this, and in particular, even if I pass in an empty list (
.modifyDF = list()), the Image column in the resulting HTML is now empty. How can I pass in
.modifyDF and also preserve the generation of the stripplot images?