j-andrews7 / ibet Goto Github PK
View Code? Open in Web Editor NEWinteractive Bioinformatics Exploratory Tools
License: Other
interactive Bioinformatics Exploratory Tools
License: Other
Break out UI and server elements where possible. Move plot functions out of main app code.
This may be why the annotation colors go back to random as well.
Genericize to "x-axis" and "y-axis" datasets to minimize width.
Hello @j-andrews7 ,
I followed the README and ran shinyPCAtools
, shinyDESeq2
, and shinyDECorr
. Both shinyPCAtools
and shinyDECorr
showed amazing interactive views and I will try them on my project datasets.
However, shinyDESeq2
gave me the following error:
Error in DESeq2::lfcShrink(dds, coef = coef, lfcThreshold = lfcThreshold) : coef %in% resultsNamesDDS is not TRUE
I proceeded as follows and got it running:
> resultsNames(dds)
[1] "Intercept" "cell_N061011_vs_N052611" "cell_N080611_vs_N052611" "cell_N61311_vs_N052611"
> colData(dds)
> res = results(dds)
> shinyDESeq2(dds, res=res, coef = "dex_trt_vs_untrt", annot.by = c("cell", "dex"))
Even though R documentation for res
says "If not provided, it will be generated from the dds object via lfcShrink or results and coef", but shinyDESeq2
did not run without that.
I know its a minor issue, just thought of letting you know in case someone else try it. :-)
Thanks.
Gurpreet
Matrix filtering error somewhere.
Initial heatmap annotated properly.
Build in a check,
For easier swapping/comparison between datasets.
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