Issue formulas of gene names with [-] (MT-ND1 + MT-CO1) do not plot

[quiquemedina]

December 10th, 2021

Greetings!

When querying with signatures (formulas containing gene names), if the gene names contain the separator “–”, example (MT-ND1 + MT-CO1), the APP does not provide plot outputs for signatures nor generate the corresponding data frames (blank output)
Notably, the individual genes plot fine, but their signatures (+, -, *. /, etc.) do not plot.

See the attachments for two examples.

Regards,

Issue formulas of gene names with [-] (MT-ND1 + MT-CO1) do not plot.pdf
Enrique

[ShixiangWang]

Hi

Could you make sure you are using the latest version？And see if the problem still occur？

remotes::install_github("openbiox/UCSCXenaShiny")

[ShixiangWang]

Also，please make sure set space between operators. We use space to detect if the user input a signature instead of a gene

[quiquemedina]

Dear Shixiang, Yes, I am using the last version (UCSCXenaShiny v1.1.4 based on UCSCXenaTools v1.4.7) and the issue remains. The problem is using formulas with gene names with "-" in them [(MT-ND1 + MT-CO1)] (spacing the operator plus). When using the genes separately MT-ND1 or MT-CO1, I get a plot, but when using both names in a formula, I get no plot. Enrique

[ShixiangWang]

@quiquemedina Thanks for your feedback. I will check ASAP and get back to you. :)

[ShixiangWang]

The issue is caused by the failed parse of the input expression:

The two genes are splitted into different part because it has - symbol.

> all.vars(parse(text = "MT-ND1 + MT-CO1"))
[1] "MT"  "ND1" "CO1"

In R, we have to use ` to avoid this.

> all.vars(parse(text = "`MT-ND1` + `MT-CO1`"))
[1] "MT-ND1" "MT-CO1"

So you should input using the second way.

Also you need to reinstall the package from GitHub again.

[ShixiangWang]

A new version is released on CRAN. You can directly install the latest version from CRAN with install.packages soon.

[quiquemedina]

I see. Querying for signatures as recommended above is now plotting just fine.

Thank you for the explanation.

Enrique