RNA expression visualization in ENCODE

Gene expression matrix

    JSON file generated by CRG:

        {
      "ensembl_id" : "ENSG00000000003.10"
      "expression_values" : [
         {
            "rep2_tpm" : 1.33,
            "rep1_fpkm" : 6.86,
            "rep1_tpm" : 2.78,
            "dataset" : "ENCSR000AAA",
            "rep2_fpkm" : 6.02
         },
         {
            "rep2_tpm" : 2.09,
            "rep1_fpkm" : 32.02,
            "rep1_tpm" : 13.7,
            "dataset" : "ENCSR000AAB",
            "rep2_fpkm" : 14.48
         },

        ...


DCC collections

    Extensive metadata associated with each dataset (aka experiment).


One expression TSV table per gene

Example (ENSG00000000003.10.expression.tsv):

accession biosample_term_name biosample_type developmental_slims fpkm * library.nucleic_acid_term_name organ_slims tpm * ...
ENCSR000AAA aortic smooth muscle cell primary cell mesoderm 6.44 RNA blood vessel 2.055 ...
ENCSR000AAB bladder microvascular endothelial cell primary cell mesoderm 23.25 RNA blood vessel,urinary bladder 7.895 ...
ENCSR000AAC smooth muscle cell of bladder primary cell mesoderm 10.675 RNA urinary bladder 2.57 ...
ENCSR000AAD bronchial epithelial cell primary cell endoderm 6.355 RNA bronchus 1.04 ...
ENCSR000AAE bronchial smooth muscle cell primary cell endoderm,mesoderm 12.72 RNA bronchus 2.995 ...
ENCSR000AAF endothelial cell of coronary artery primary cell mesoderm 18.115 RNA blood vessel,heart 4.965 ...
ENCSR000AAG smooth muscle cell of the coronary artery primary cell mesoderm 10.775 RNA blood vessel,heart 3.11 ...
ENCSR000AAH regular cardiac myocyte primary cell mesoderm 16.65 RNA NA 1.88 ...
ENCSR000AAI dermis blood vessel endothelial cell primary cell ectoderm,mesoderm 28.08 RNA blood vessel,skin of body 8.415 ...
... ... ... ... ... ... ... ... ...

* averaged across replicates


One set of interactive box-plots per gene

Interactive box-plots are generated by feeding the expression TSV to R's plotly library. The R script takes the following parameters:   

Parameter Possible values
$geneId Any ensembl_id
$metrics
 'tpm' or 'fpkm'
$colorBy
 Any column name of the input TSV
$groupBy
 Any column name of the input TSV

Generic R code:    

library(plotly)
plot <- read.table("$geneId.expression.tsv", header=T, as.is=T, sep="\t")
figure<-plot_ly(plot, x=$groupBy, y=log10($metrics+0.01), color=$colorBy, type="box", boxpoints = "all", jitter = 0.3, pointpos = -1.8) %>%
 layout(
        title="$geneId / $groupBy vs $colorBy",
        margin= list(b=300)
        )
htmlwidgets::saveWidget(plotly:::toWidget(figure), "./$groupBy.vs.$colorBy.$geneId.html", selfcontained = FALSE)

Examples of parameter combinations

Input:
Parameter Assigned value
$geneId ENSG00000000003.10
$metrics
 tpm
$colorBy
 library.nucleic_acid_term_name
$groupBy
 organ_slims

Output:
Input:
Parameter Assigned value
$geneId ENSG00000000003.10
$metrics
 tpm
$colorBy
 system_slims
$groupBy
 biosample_term_name

Output:
Input:
Parameter Assigned value
$geneId ENSG00000000003.10
$metrics
 tpm
$colorBy
 organ_slims
$groupBy
 system_slims

Output:
Input:
Parameter Assigned value
$geneId ENSG00000000003.10
$metrics
 tpm
$colorBy
 biosample_type
$groupBy
 organ_slims

Output:

Given a $geneId, is it possible to let the user choose $metrics, $groupBy and $colorBy dynamically (via some JavaScript magic)?

Plotly interactive plots embed only some data (i.e.,keeps data only for the concerned columns, and ditches everything else), so, a priori, no.

(there might be a workaround I'm not aware of, though).

I have made some tests with Shiny, another R library compatible with plotly (see screenshot below).

It seems powerful enough, unfortunately sharing options are not great.




Contact: Julien Lagarde (julien.lagarde AT crg.eu)