image orientation squeezes in shiny display

[dschneiderch]

It looks like the rosette carousel is expecting landscape images. when using portrait images it creates white space which makes everything smaller than it needs to be and hard to see.

it would be nice to also have a choice how many images to view next to each other. on my labtop 3 I'd say I have room for 3 but on my external monitor i could probably comfortably view 6 or more.

in the rosette explorer it squeezes the images unnaturally

[phue]

Thanks for reporting this! I have to say that our images where always more or less quadratic, so I never noticed that.

it would be nice to also have a choice how many images to view next to each other. on my labtop 3 I'd say I have room for 3 but on my external monitor i could probably comfortably view 6 or more.

Totally agree, I will look into it. Probably this can be made responsive to screen size.

[phue]

I made some changes to address this:

• e8872c0 should fix the distorted images
• f81c561 adds breakpoints that change the number of images in the carousel according to screen width

It would be great if you could give this a try and let me know if it looks better now. The changes are on the dev branch, so to run it you would have to tell nextflow to use it like so:

nextflow run Gregor-Mendel-Institute/aradeepopsis -r dev ...

[dschneiderch]

i will try this on Friday

[dschneiderch]

I actually have time today but I was hoping to just run the new shiny app, if possible.
I ran the nextflow on the server and copied results to my computer to run the shiny.

I tried docker run -v $(pwd):/mnt/shiny -p 44333:44333 beckerlab/aradeepopsis-shiny:dev R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')" so it downloads a different image labeled dev from dockerhub but I see the same issues.

[dschneiderch]

I copied the contents from dev branch app.R to my output directory and reran the docker.

I don't see a difference in the carousel

The rosette explorer looks perfect

although the color channels tab is quite stretched. I don' tknow if you can specify a max width, or you could increase the height. or leave it as good enough :-) It compresses when the window is resized.

rosette experiment

This was confusing because at first I got a new error:
I get a new error that looks like the data tried to join with itself. I double checked my file and I only have 1 class_norm_area and it is of type double.

I noticed on line 29 of app.R you are reading in a fixed filename so I realized you are reading the original datafile and attempting to join the metadata. I actually only need to provide the metadata and not the traits themselves. I would suggest adding a note in the popup that no columns from the traits file should be in the metadata file except file

now it looks pretty good!

the one exception is that it doesn't recognize the factors as factors and instead orders them alphanumerically. I realize this is a constraint of saving to csv so i'm not sure how you'd improve that functionality.

[dschneiderch]

also, the yellow is pretty hard to see. I've found a background color of 'grey40' to work pretty well as a compromise for both dark and light colors.

[phue]

I don't see a difference in the carousel

The number of images should now scale according to screen size. I can't do much about the whitespace between the images, that is how slickR renders the carousel thing and I can't seem to find an option to control this.

the color channels tab is quite stretched

I changed the plot to be 600x600 and also increased the image size in the rosette explorer to be consistent

note in the popup that no columns from the traits file should be in the metadata file except

Good point, I added something like that. I guess it was not clear enough that the metadata is joined with the pipeline output.

yellow is pretty hard to see

True, I changed the color map slightly and increased the line thickness

Thanks for your suggestions!