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PediatricOpenTargets / OpenPedCan-api

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Add boxplots to the sides of differential gene expression heatmaps #61

Closed logstar closed 1 year ago

logstar commented 2 years ago

Add boxplots to the sides of differential gene expression (DGE) heatmaps that are transferred by /dge/top-gene-disease-gtex-diff-exp/plot and /dge/gene-all-cancer-gtex-diff-exp/plot endpoints.

Following is the plan to implement the boxplots:

If you have any questions or suggestions, feel free to message me or leave comments in this issue.

cc @afarrel @chinwallaa @taylordm

logstar commented 2 years ago

@afarrel @taylordm @chinwallaa - It takes about 6 seconds to query the TPM values of 50 top genes of required cancer and GTEx samples.

I will continue working on generating the boxplots, although 6 seconds have exceeded the expectation that each plot should take less than 5 seconds. After the heatmaps with boxplots on the sides are implemented, I will create a new issue to discuss potential efficiency optimizations.

@sangeetashukla has been updating DGE results with v10 data. The corresponding issue and progresses are reported at https://github.com/PediatricOpenTargets/ticket-tracker/issues/273.

Let me know if you have any questions or suggestions.

logstar commented 2 years ago

@taylordm @afarrel @chinwallaa - I will add a parameter to determine whether to include boxplot or not in the DGE heatmaps, as discussed in 01/19/2021 meeting.

logstar commented 2 years ago

@taylordm @afarrel @chinwallaa - Following are two example one-EFO DGE heatmaps with boxplots on the right side. The plotting procedure is adapted from @afarrel's code. There is no boxplot for columns, because rows have different genes.

hmbp2 hmbp1

logstar commented 2 years ago

@taylordm @afarrel @chinwallaa - Following are two example one-ENSG DGE heatmaps with boxplots on the top and right sides. The plotting procedure is adapted from @afarrel's code.

I will be working on the following items:

hmbp1

hmbp2