Adding gene_var module with lollipop plot #10
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Update README.md
more tidying
update master
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This looks great! For prototyping purposes, can you make the data files much smaller (<5mb?). It takes a really long time to load the app - for an app in production this actually isn't that big of a deal because it only has to load once running on a server, but for working on the app it makes it a lot slower to test small changes.
I'd suggest just filtering the files down to something like: NF1, NF2, PTEN, SUZ12, EED, KRAS, NRAS, P53 for starters.
Side note, I got this warning for one of the ORFs:
Warning: Error in maftools::lollipopPlot: Structure for protein C1orf170 not found.
[No stack trace available]
Not sure where this Rproj file is coming from, but the project file is already in the root directory.
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| output$lollipop_plot <- shiny::renderPlot({ | ||
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| maftools::lollipopPlot( |
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this function seems to be printing to console, if this can be turned off that might speed stuff up a bit (especially when we scale up to bigger files)!
1: HES4 NM_021170 NP_066993 221
2: HES4 NM_001142467 NP_001135939 247
Using longer transcript NM_001142467 for now.
I just fixed this code chunk, before it had no helpful information, sorry! |
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Thanks! That error is being thrown because maftools cant find a mapped protein structure of the gene C1orf170 to plot the lollipops on! Looking into how to fix that... |
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starting a new pull request due to some push hiccups. |
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