Expression in cell type (%)

[h1hui]

Hi there,

Thank you for doing such a good job developing this library.

I was reading the reference paper: Skene, et al. Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment.Front. Neurosci, 2016.

And I would like to plot the same expression in celltype (%) plot, but how can I do it with the development version of this library? Is it still a feature?

Thanks, Ashley

[bschilder]

I think this might be what you're looking for: https://nathanskene.github.io/EWCE/reference/generate_bootstrap_plots.html

[h1hui]

Thank you for your reply. However I ran into an error while plotting.

> plot_file_path <- EWCE::generate_bootstrap_plots(
+     sct_data = ctd,
+     hits = hits,
+     genelistSpecies = "human",
+     sctSpecies = "human",
+     output_species = "human",
+     method = "homologene",
+     reps = 1000,
+     annotLevel = 1,
+     full_results = full_results,
+     listFileName = "",
+     savePath = tempdir(),
+     verbose = TRUE
+ )
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
Aligning celltype names with standardise_ctd format.
Error in exp_mats[[cc]][s, ] <- sort(expD[, cc]) : 
  number of items to replace is not a multiple of replacement length

Where do you suggest the problem lies?

Thanks, Ashley

[NathanSkene]

Have you tried it using the example datasets?

From: h1hui @.> Date: Friday, 13 May 2022 at 20:00 To: NathanSkene/EWCE @.> Cc: Subscribed @.> Subject: Re: [NathanSkene/EWCE] Expression in cell type (%) (Issue #63) This email from @. originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Thank you for your reply. However I ran into an error while plotting.

plot_file_path <- EWCE::generate_bootstrap_plots(

• sct_data = ctd,

• hits = hits,

• genelistSpecies = "human",

• sctSpecies = "human",

• output_species = "human",

• method = "homologene",

• reps = 1000,

• annotLevel = 1,

• full_results = full_results,

• listFileName = "",

• savePath = tempdir(),

• verbose = TRUE

• )

Retrieving all genes using: homologene.

Retrieving all organisms available in homologene.

Mapping species name: human

Common name mapping found for human

1 organism identified from search: 9606

Gene table with 19,129 rows retrieved.

Returning all 19,129 genes from human.

Standardising sct_data.

Converting to sparse matrix.

Converting to sparse matrix.

Aligning celltype names with standardise_ctd format.

Error in exp_mats[[cc]][s, ] <- sort(expD[, cc]) :

number of items to replace is not a multiple of replacement length

Where do you suggest the problem lies?

Thanks, Ashley

— Reply to this email directly, view it on GitHubhttps://github.com/NathanSkene/EWCE/issues/63#issuecomment-1126357484, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AH5ZPE5Y22VJUXY4F2TWE7DVJ2RENANCNFSM5VV2OZBQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[h1hui]

Yes I tried. It ran without a problem, but I still don't know what's causing the error in my dataset.

[bschilder]

@h1hui please follow the Bug template provided when you submit a new issue. That way, you can see the steps necessary to provide a reproducible example

[bschilder]

Looks like you started a new Issue on this topic #66 . Closing this one to avoid redundancy

[NathanSkene]

Hey,

Pretty sure it’s still implemented in this function:

https://github.com/NathanSkene/EWCE/blob/master/R/generate_bootstrap_plots.r

Been a good while since I’ve used it though, so do let me know if I’m wrong.

Best,

Nathan

From: h1hui @.> Date: Wednesday, 11 May 2022 at 19:34 To: NathanSkene/EWCE @.> Cc: Subscribed @.> Subject: [NathanSkene/EWCE] Expression in cell type (%) (Issue #63) This email from @. originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Hi there,

Thank you for doing such a good job developing this library.

I was reading the reference paper: Skene, et al. Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment.Front. Neurosci, 2016.https://www.frontiersin.org/articles/10.3389/fnins.2016.00016/full

And I would like to plot the same expression in celltype (%) plot, but how can I do it with the development version of this library? Is it still a feature? [Screen Shot 2022-05-11 at 11 34 22 AM]https://user-images.githubusercontent.com/33336127/167921490-1b2d27c7-5181-4588-9c1e-4c1b6c625a0d.png

Thanks, Ashley

— Reply to this email directly, view it on GitHubhttps://github.com/NathanSkene/EWCE/issues/63, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AH5ZPEZLFQFTZC6JJ2VVKF3VJP4U3ANCNFSM5VV2OZBQ. You are receiving this because you are subscribed to this thread.Message ID: @.***>