alosdiallo/dna_rchitect

A Shiny App for visualizing genomic data

dna_rchitect's Issues

Add pdf tutorial to site

Add the pdf tutorial to the site

Download all as PDF for network did not work

Did not seem to display the PDFs in google chrome.

If you do not select colors the box should be red

If you do not select colors the box should be red indicating that this is missing

Change: An error has occurred. Check your logs or contact the app author for clarification.

Change: An error has occurred. Check your logs or contact the app author for clarification.
To: An error has occurred. Please make sure that the settings for your genes/area of interest are correct.

Change header text

Change the text in the Header section to read" Does your data contain a header? Yes or No"
Have a yes or no checkbox for the user to select.

change help button

Change the help button to say "Interactive Tutorial".

Gene font size

Since we typically zoom out and include many genes in the bezier curve plots, is there a way to reduce the gene label font size?

Header check does nothing

The site should not require a header. Ask the user if they have a header or not. If not don't require a header.

Add to the site: Tcon_Immgen_3.bg Treg_Immgen_3.bg

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100738
I have the the files but will add.

Remove arrows on network plot

Remove arrows on network plot

Load sample data

This is done, I will apply the changes to the qa version later in the day.

What I want to make sure here is that whenever the user runs the app, the chosen type of file by default is HiC, and then the user can load data. If the user chooses ATAC and then decides to load sample data, should there be different types of data to load other than the ones which were there while HiC was chosen? Or no matter what the user chooses the sample data to load should be fixed?

Add sushi heatmap

Add the sushi heatmap

You can't load more than 1 dataset

You can't load more than 1 dataset. If you try it crashes.

Download XGMML does not download the correct file

When I download the XGMML file on the QA site it does not download the proper file. It downloads some html.

Edge overlap issue in network output

When using the K562 data, the network does not allow for multiple edges to the same nodes to be seen. In short, the edges overlap each other. We need to allow for both edges to be seen. In the example shown, the bottom edge is grey and red (can see red highlight underneath), while the edge on top is only grey.

Loading ImmGen_T.Nve.Sp.ATAC.bg plus hic_bedpe.txt leads to an infinite loop of connecting and disconnecting

If you load ImmGen_T.Nve.Sp.ATAC.bg then later try to load another dataset via upload the app goes into an infinite loop. Where it tries to connect then disconnect over and over again.

create network using Visnetwork package

Regarding the network, we have the following:

• interactive network
• Having the option to edit the network (delete node/add node/edge)
• save the network in html file (so that when it is saved as html file, it will remain interactive)

I will deploy the above changes to the qa version later in the day.

If you fail to pick a color the app fails, if you then select colors it is nothing happens when you select submit perimeters

Production version
If you fail to pick a color the app fails, if you then select colors it is nothing happens when you select submit perimeters

.

Interactive tutorial and reload app should be on the same line

Interactive tutorial and reload app should be on the same line

species info not listed

In the app under genomes the version are not listed. Please list them.
mouse mm10
human Hg38
drosophila_melanogaster Release 6

Fix Y axis

Have the title not too close to the axis

Select colors for bezier curves should say "Select color for data"

Select colors for bezier curves should say "Select color for data"

Include an option for choosing colors for the bezier curves

network names should match Publication figure

Network should say: Genomic Network
Hubs should say: Network Hubs
Groups should say: Community Detection

Change text for Download HiC Plot to "Download Bezier Curve Plot"

Change text for Download HiC Plot to "Download Bezier Curve Plot"

clicking head or tail does not change the view

Clicking head or tail does not change the view. This was tested on chrome.

Tie in sample data to experiment type

Attack Seq data should show then selected, hic data should show when selected.

Put download HiC Plot below plot

Put download HiC Plot below plot

Download plot as pdf

Download the plot as a pdf

The interactive tutorial button is covered up by the reload app button

The interactive tutorial button is covered up by the reload app button

Datasets other than K562 are broken

Datasets other than K562 are broken

Error message to check logs must be removed

Error message to check logs must be removed

Chip-seq sample data needs citation information

Chip-seq sample data needs citation information

Shiny online app is hanging frequently ? some files missing in local installation

HI

I am trying to use DNA_Rchitect for my data but some files are missing from the source code installation. Installation is not happening correctly, Installation is available from bioconductor/bioconda ? Also online server is hanging frequently? One more question for RNA data, does to require normal count data with gene name or gene coordinate, I could not find RNA data example file on online app.

Thanks

Arpit

Update the logo

Update the logo

The pdf fails to load when I click on the help button.

The pdf fails to load when I click on the help button.

K562 data labeling on DNA_Rchitect

In the drop down for loading, it says Human mouse. The K562 data set is only loading Human.
The study also has mouse data.

Make help document

Use the pdf that Ricardo made as the help page. Work with Ricardo to get an updated pdf.

Adjust position of plots for Attack seq

Adjust the positions of the plots so that you don't have to scroll to view them.

List the organism for the sample data

Right now when you load the sample data it does not list the type of organism.

Accept Data without a header

Accept Data without a header

Have 1 button to download all plots on the left

Have 1 button to download all plots on the left for both pdf and svg

Accept any text in header

Right now the code looks for specific text. What we should do is require info to be in specific columns and allow for any header.

Color not changing with HIC single data type

Color not changing with HIC single data type

Loading sample data after sample data was loaded required re-fresh

I tried to load sample data after a dataset was loaded and visualized. The sample data did not load and required a re-fresh.

Make sure interactive tutorial works

Run through the interactive tutorial and make sure it works

Add new datasets

Add Hg19 and MM9

Loading sample data does not display information about the dataset

Loading sample data does not display information about the dataset

Download svg crops out y axis name

Download svg crops out y axis name