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gexijin / idepGolem

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multiple issues still exist #588

Open JianYes opened 11 months ago

JianYes commented 11 months ago

Is your feature request related to a problem? What value do you see this adding? Please describe.

PCA: error message in PCAtools subtab at the bottom if data have more than 2 factors.(issue #540) DEG2: scatter plot has label option now. But it won’t work if been asked to label in ensembl gene ids. (issue #537) Pathways: 1 The note at the bottom of KEGG diagram still uses green(blue) for up and red(orange) for down. 2 We still have no download options for significant pathway, Tree, Network, and KEGG.(issue #531) 3 Complete the report in Pathway tab.(issue #566) Bicluster: 1 Now we can select the cluster at the left side of the tab, do we still need the window of “cluster” in Enrichment tab? Or we can show the cluster number if we keep the window. .(issue #523) 2 Is it suitable using “Cluster” as agenda for tree plot in Enrichment sub tab? Network: 1, 2, 3 Similar problems as Bicluster, extra cluster window and “Cluster” agenda. 4 We can download tables now, but “Download network for selected module” have the same table as “Download all modules”. (issue #526). Now both of them are network for the selected module. No table for ALL modules is available. 5 Add download options for “Network plot” and “Module plot”. (issue #526)

gexijin commented 11 months ago

I was unable to reproduce the PCA error. Please double check.

gexijin commented 11 months ago

The issue on DEG2 is also fixed. Enesembl gene IDs are labelled correctly.

gexijin commented 11 months ago

Pathway 1. Red green. Fixed.

JianYes commented 10 months ago

I was unable to reproduce the PCA error. Please double check.

I checked it. Now the error is gone.

ChrisTret commented 9 months ago

Currently working on issue #531

ChrisTret commented 9 months ago

531 Added download for Significant pathway, tree, and KEGG. It appears Network already has a .jpeg download button.

JianYes commented 9 months ago

Great job, Chris!

JianYes commented 8 months ago

Can we put the .jpeg download button for Network on the top of the plot? It's uneasy to notice the button on the bottom.

JianYes commented 8 months ago

I was unable to reproduce the PCA error. Please double check.

Please use Mouse, 2*2 demo data to reproduce the PCA error.

JianYes commented 8 months ago

The issue on DEG2 is also fixed. Ensembl gene IDs are labelled correctly.

Ensembl gene IDs are labelled correctly for Volcano and MA plots, but not for Scatter plot.

gexijin commented 8 months ago

I was unable to reproduce the PCA error. Please double check.

Please use Mouse, 2*2 demo data to reproduce the PCA error.

The PCA error is fixed. See you comment above on Oct. 16. The issue was closed.

JianYes commented 8 months ago

I was unable to reproduce the PCA error. Please double check.

Please use Mouse, 2*2 demo data to reproduce the PCA error.

The PCA error is fixed. See you comment above on Oct. 16. The issue was closed.

If I use Mouse; 2*2 factor demo data, I will get the attached PCAtools tab: image

gexijin commented 8 months ago

OK. It does not show up when I tried. Please reopen that issue. #540.

Try not to comment here. But comment on the individual issues. We can use this as a reference.