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Check notebook chunk #553

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sjspielman opened this issue Sep 22, 2022 · 1 comment
Open

Check notebook chunk #553

sjspielman opened this issue Sep 22, 2022 · 1 comment

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@sjspielman
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There is something that needs to be fixed with this chunk, but I only wrote down in my notes was "check plot_marker_expression chunk" in my notes, and I don't precisely remember what I meant! But, @jashapiro should know.

```{r plot_marker_expression, live = TRUE}
# get gene id and gene symbol for nicer plotting
rank <- 1
gene_id <- gene_info$ID[1]
symbol <- gene_info$Symbol[1]
# Plot UMAP results colored by expression
plotReducedDim(hodgkins_sce, "UMAP",
colour_by = gene_id) +
# label the guide with the gene symbol
guides(color = guide_colourbar(title = symbol))
```

Noting also this is the chunk where we saw, as mentioned in #550, that we don't want to be labeling UMAP legends with labs().

@jashapiro
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Thank you for noting this! The error is that the gene_id and symbol definitions should use rank rather than hard coding!

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