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kstreet13 / bioc2020trajectories

Trajectory inference and differential expression over multiple conditions in scRNA-seq
https://kstreet13.github.io/bioc2020trajectories/
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there is no package called ‘bioc2020trajectories’ #5

Closed guilingma closed 2 years ago

guilingma commented 2 years ago

Hi bioc2020trajectories official,

When I am following your workshop on the trajectory analysis:

scores <- bioc2020trajectories::imbalance_score(

_Error in loadNamespace(x) : there is no package called ‘bioc2020trajectories’**_

It says, there is no bioc2020trajectories.

I load all the library required according your workshop instruction.

Thank you very much for your help. Guiling

kstreet13 commented 2 years ago

Hello @guilingma,

My guess is that this was caused by some sort of error in the package installation. What happens when you run BiocManager::install('kstreet13/bioc2020trajectories')?

Best, Kelly

guilingma commented 2 years ago

Hi Kelly, Thank you very much, the bioc2020trajecctoreis works now. However, I have two questions below:

Would you like to help me again? Thank you very much.

Qustion1: set.seed(3)

icMat <- evaluateK(counts = as.matrix(assays(sce)$counts),

  • pseudotime = colData(sce)$slingshot$pseudotime,
  • cellWeights = colData(sce)$slingshot$cellWeights.V1,
  • conditions = factor(colData(sce)$pheno$treatment_id),
  • nGenes = 300,
  • k = 3:7) Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments. Question 2: When I skip the above code, and do the Fit GAM section: It seemed the [Fit GAM] section will take ~an hour, is this normal, or there is any optional code for this section? ​ Thank you very much Guiling Ma

    From: Kelly Street @.> Sent: Monday, March 14, 2022 9:49 To: kstreet13/bioc2020trajectories @.> Cc: Ma, Guiling @.>; Mention @.> Subject: Re: [kstreet13/bioc2020trajectories] there is no package called ‘bioc2020trajectories’ (Issue #5)

Hello @guilingmahttps://urldefense.com/v3/__https://github.com/guilingma__;!!JmPEgBY0HMszNaDT!_ATP-M-VObJssrYz1-qsUpGqRns0rMaDxkpoKtXqp735Uqgd_Kugkoy_7_iXs36RnQ$,

My guess is that this was caused by some sort of error in the package installation. What happens when you run BiocManager::install('kstreet13/bioc2020trajectories')?

Best, Kelly

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/kstreet13/bioc2020trajectories/issues/5*issuecomment-1066979519__;Iw!!JmPEgBY0HMszNaDT!_ATP-M-VObJssrYz1-qsUpGqRns0rMaDxkpoKtXqp735Uqgd_Kugkoy_7_j7tv9xaw$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AIB2TH2DWCAOTGFKSIV76UDU75NZLANCNFSM5QQHLJNQ__;!!JmPEgBY0HMszNaDT!_ATP-M-VObJssrYz1-qsUpGqRns0rMaDxkpoKtXqp735Uqgd_Kugkoy_7_iU3iGNoA$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!JmPEgBY0HMszNaDT!_ATP-M-VObJssrYz1-qsUpGqRns0rMaDxkpoKtXqp735Uqgd_Kugkoy_7_iG9e994g$ or Androidhttps://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!JmPEgBY0HMszNaDT!_ATP-M-VObJssrYz1-qsUpGqRns0rMaDxkpoKtXqp735Uqgd_Kugkoy_7_hl0Kt4ig$. You are receiving this because you were mentioned.Message ID: @.***>

kstreet13 commented 2 years ago

Hi @guilingma,

This is probably due the the way that tradeSeq handles input data from slingshot. The more recent version of the workshop may have fixed this issue, but when we changed slingshot to use PseudotimeOrdering objects, it broke some of the older code.

You should be able to get around it by substituting the appropriate accessor functions, which are always kept up-to-date. If you replace colData(sce)$slingshot$pseudotime with slingPseudotime(sce) and colData(sce)$slingshot$cellWeights.V1, with slingCurveWeights(sce), then I think it should work.

And yes, unfortunately, this step is a little slow. It's something we're aware of, but unsure of how to fix, at the moment.

Best, Kelly

guilingma commented 2 years ago

Hi Kelly,

Thank you very much for your answer.

It worked well.

Have a great day.

Guiling

From: Kelly Street @.> Sent: Tuesday, March 15, 2022 11:55 To: kstreet13/bioc2020trajectories @.> Cc: Ma, Guiling @.>; Mention @.> Subject: Re: [kstreet13/bioc2020trajectories] there is no package called ‘bioc2020trajectories’ (Issue #5)

Hi @guilingmahttps://urldefense.com/v3/__https://github.com/guilingma__;!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZqwdj_u_g$,

This is probably due the the way that tradeSeq handles input data from slingshot. The more recent version of the workshophttps://urldefense.com/v3/__https://hectorrdb.github.io/bioc2021trajectories/__;!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZrogIr56A$ may have fixed this issue, but when we changed slingshot to use PseudotimeOrdering objects, it broke some of the older code.

You should be able to get around it by substituting the appropriate accessor functions, which are always kept up-to-date. If you replace colData(sce)$slingshot$pseudotime with slingPseudotime(sce) and colData(sce)$slingshot$cellWeights.V1, with slingCurveWeights(sce), then I think it should work.

And yes, unfortunately, this step is a little slow. It's something we're aware of, but unsure of how to fix, at the moment.

Best, Kelly

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/kstreet13/bioc2020trajectories/issues/5*issuecomment-1068284402__;Iw!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZot6AxtTA$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AIB2TH354PRIDHD3YXY7UTDVADFJ3ANCNFSM5QQHLJNQ__;!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZqlNljaiA$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZrefJMihQ$ or Androidhttps://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!JmPEgBY0HMszNaDT!-0VvgItS5rM7VT0kjlTW8aXjOSnKM73N6uh2cmJJO4huMGiEqfeVnE9NJZqiebOuFQ$. You are receiving this because you were mentioned.Message ID: @.***>