Gate not reflected as I did

[ryotasato2]

gates used to work properly but suddenly all the gate I made were shown on the left top with smaller size. Is this a bug or am I doing something wrong? Below is my code and error message. Thx!

harmonized_gated1 <-
harmonized_seurat %>%
mutate(gated1 = tidygate::gate_chr(
UMAP_1, UMAP_2, .color = seurat_clusters,
.size = 0.1
))
Mark region on plot.
Error in dplyr::mutate():
ℹ In argument: gated1 = tidygate::gate_chr(...).
Caused by error in map():
ℹ In index: 1.
Caused by error in data[i, 1]:
! subscript out of bounds
Run rlang::last_trace() to see where the error occurred.

[stemangiola]

gates used to work properly but suddenly all the gate I made were shown on the left top with smaller size. Is this a bug or am I doing something wrong? Below is my code and error message. Thx!

harmonized_gated1 <- harmonized_seurat %>% mutate(gated1 = tidygate::gate_chr( UMAP_1, UMAP_2, .color = seurat_clusters, .size = 0.1 )) Mark region on plot. Error in dplyr::mutate(): ℹ In argument: gated1 = tidygate::gate_chr(...). Caused by error in map(): ℹ In index: 1. Caused by error in data[i, 1]: ! subscript out of bounds Run rlang::last_trace() to see where the error occurred.

Rstudio keeps making the interactive backend in base R buggy. Within the #tidyomics community, we would like to change the backend to a more proper one.

https://github.com/orgs/tidybiology/projects/1

Chances are if you use another Rsrudio, from your laptop, for example it would work. Or update Rstudio.

Or contribute to changing the backend to a more modern one! It is a very nice project. The new backend should improve efficiency and scalability as a separate goal. @LiNk-NY might have ideas.

#20

[LiNk-NY]

@ryotasato2
Do you have a reproducible example that we can run? It would kickstart any movement in this space. Thank you!

[stemangiola]

This is the issue in the Rstudio repository

rstudio/rstudio#10025
rstudio/rstudio#12682

An option could be to use a more modern interactive gating library; the the folks in Rstudio seem not to be so responsive with this.

[stemangiola]

New interface with modern visualisation, which avoid this issue is coming.