hwlim / scrnaseq-interactive-apps

scRNAseq-interactive-apps

Collection of interactive utility for single cell data in Lim Lab @ CCHMC

scrnaseq-interactive-apps's Issues

Functional suggestions

Can we provide seurat object file selection so that user decide the input file?
by adding file selection menu?

Currently, the shiny app assumes specific seurat object file name. But user may have different file name. It would be great if user can choose the input file.

Is there a way to run the shiny app in the bash command line? like
bash>> shiny_feature.R <path/to/seurat.rds>
I guess it may be possible if we put the contents of the shiny app file into a usual command line script like we already have?

Also, it would be convenient to add required package installation step like you already did for shiny, including
e.g. Seurat.

default gene list upon start up

Currently, default gene list is not working upon start up.
For example, it would be good to display feature plot for a few house keeping genes such as "Gapdh" and "Actb".
But the gene symbols can be different by organism, e.g. Gapdh vs GAPDH.
So it would be checked against the gene list from the seurat object and automatically entered in the gene list menu.

Aslo, please note that I commented out

features = eventReactive(input$assay,
{
rownames(seurat_object@assays[[input$assay]])
}
)

Still everything work fine the same way and everthing is handled by subsequent observeEvent block.
I guess there's a bit of redundancy and difference between eventReactive and observeEvent.