Display issues with heatmap generated

[garffy]

I was using the d3heatmap library to generate the cluster and heatmap for a dataset with 11374 records, and 8 variables as the clustering criterion.

As seen in the attached screenshot, the heatmap does not show any colour, even though upon mouseover, we can see its corresponding value of a particular cell in a heatmap.

How can we overcome this issue? Thanks

Hardware and software specs:

1. Intel Processor i5-4200 with 8GB RAM
2. Windows 7 OS
3. R version 3.1.2
4. R studio Version 0.98.1103

[Liuy12]

I have the similar issue now. d3heatmap is working fine in my console but not in a shinyapp. In my shinyapp, I encountered similar issue as explained above. The difference is that the main heatmap (except row and col dendrogram) is not plotted, neither can I see any values. It is just not printed.

My session information is as follows,

n_US.UTF-8
tz America/Chicago

Packages ------------------------------------------------------------------- package * version date
acepack 1.3-3.3 2014-11-24 annotate 1.47.4 2015-07-20 AnnotationDbi 1.31.17 2015-06-18 assertthat 0.1 2013-12-06 base64enc 0.1-3 2015-07-28 Biobase * 2.29.1 2015-05-03 BiocGenerics * 0.15.6 2015-08-08 BiocParallel 1.3.48 2015-08-05 chron 2.3-47 2015-06-24 cluster 2.0.3 2015-07-21 colorspace 1.2-6 2015-03-11 curl 0.9.2 2015-08-08 d3heatmap * 0.6.1 2015-08-14 data.table * 1.9.4 2014-10-02 DBI 0.3.1 2014-09-24 Delaporte 2.2-3 2015-07-01 DESeq * 1.21.0 2015-04-17 DESeq2 * 1.9.27 2015-08-13 devtools * 1.8.0 2015-05-09 digest 0.6.8 2014-12-31 dplyr * 0.4.2 2015-06-16 DT * 0.1 2015-06-09 edgeR * 3.11.2 2015-05-25 foreign 0.8-65 2015-07-02 Formula 1.2-1 2015-04-07 futile.logger 1.4.1 2015-04-20 futile.options 1.0.0 2010-04-06 genefilter 1.51.0 2015-04-17 geneplotter 1.47.0 2015-04-17 GenomeInfoDb * 1.5.10 2015-08-08 GenomicRanges * 1.21.18 2015-08-08 ggplot2 1.0.1 2015-03-17 git2r 0.11.0 2015-08-12 gridExtra 2.0.0 2015-07-14 gtable 0.1.2 2012-12-05 Hmisc 3.16-0 2015-04-30 htmltools 0.2.6 2014-09-08 htmlwidgets 0.5 2015-06-21 httpuv 1.3.3 2015-08-04 httr 1.0.0 2015-06-25 IRanges * 2.3.18 2015-08-08 jsonlite 0.9.16 2015-04-11 knitr 1.10.5 2015-05-06 lambda.r 1.1.7 2015-03-20 lattice * 0.20-33 2015-07-14 latticeExtra 0.6-26 2013-08-15 limma * 3.25.15 2015-08-06 locfit * 1.5-9.1 2013-04-20 magrittr 1.5 2014-11-22 MASS 7.3-43 2015-07-16 matrixStats 0.14.2 2015-06-24 memoise 0.2.1 2014-04-22 mime 0.3 2015-03-29 munsell 0.4.2 2013-07-11 networkD3 * 0.1.8 2015-07-11 nnet 7.3-10 2015-06-29 plyr 1.8.3 2015-06-12 png 0.1-7 2013-12-03 pracma 1.8.6 2015-07-14 proto 0.3-10 2012-12-22 R6 2.1.0 2015-07-04 rCharts * 0.4.5 2015-08-12 RColorBrewer 1.1-2 2014-12-07 Rcpp * 0.12.0 2015-07-25 RcppArmadillo * 0.5.300.4 2015-08-04 reshape2 1.4.1 2014-12-06 rjson 0.2.15 2014-11-03 RJSONIO 1.3-0 2014-07-28 rpart 4.1-10 2015-06-29 RSQLite 1.0.0 2014-10-25 rstudioapi 0.3.1 2015-04-07 rversions 1.0.2 2015-07-13 S4Vectors * 0.7.13 2015-08-13 scales 0.2.5 2015-06-12 shiny * 0.12.2 2015-08-05 shinythemes * 1.0.1 2015-03-03 stringi 0.5-5 2015-06-29 stringr 1.0.0 2015-04-30 SummarizedExperiment * 0.3.3 2015-08-08 survival 2.38-3 2015-07-02 whisker 0.3-2 2013-04-28 XBSeq * 0.99.8 2015-08-10 XML 3.98-1.3 2015-06-30 xml2 0.1.1 2015-06-02 xtable 1.7-4 2014-09-12 XVector 0.9.1 2015-04-30 yaml 2.1.13 2014-06-12

[federicou]

I have the same problem putting in the same shiny app d3heatmap and rCharts. It seems they are conflicting with the D3 library. I tried the renderChart2 option that is not working at all.

[bextra]

I ran into this problem too. It's because when there are too many points the color gets washed out. If you zoom you can see that there is gradation of color. I subset my data logically to overcome this, but you could also tweak the color scheme.

[warnes]

I suspect that with the individual boxes being so small, the white grid lines are taking up all of the space.

Try setting show_grid=FALSE to omit the grid lines.