cellrouter addInfo about cellrouter HOT 15 OPEN

edroaldo commented on August 18, 2024

cellrouter addInfo

from cellrouter.

Comments (15)

edroaldo commented on August 18, 2024

Hi Kun, Thank you for your interest in CellRouter. You need to make sure that the dimensions of the raw data after creating the cellrouter object and the dimensions of the metadata table from seurat are the same. Please, try something like: data <- as.data.frame(as.matrix([email protected])) cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0) You are already doing the above... so could you pelase send me: dim([email protected]) dim([email protected]) Thanks! Em ter, 21 de ago de 2018 às 21:25, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Thanks for designing the cellrouter program. Recently, I'm try to do trajectory using it. My current data is from Seurat, but I met this error when I want to create a CellRouter object. My code is here: samples <- get(load('Paul_Cell_samples.R')) cellrouter <- CellRouter(path='Paul_Cell_data.R', min.cells=3, min.genes=0) [1] "Initializing CellRouter object" data <- ***@***.***)) cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0) [1] "Initializing CellRouter object" cellrouter <- addInfo(cellrouter, metadata = ***@***.***, colname = 'merged_20_Aug', metadata.column='res.0.8') Error in rep(colors, times = replicate_row) : invalid 'times' argument Any help will be appreciated! Thanks! Best, Kun — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqUR8DNW-RjRBjz-kG_K-juLXrXGDB0ks5uTLLzgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo,

Thanks. Here is the dimension, they are different, does this cause the error? How should I fix it? Thanks.

dim([email protected])
[1] 29408 4859
dim([email protected])
[1] 4391 34

from cellrouter.

edroaldo commented on August 18, 2024

Thanks for the information. You can do something like this: data <- as.data.frame(as.matrix([email protected][, *rownames([email protected])*)) #so, only raw data for which there is associated metadata is included. cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0) cellrouter <- addInfo(cellrouter, metadata = [email protected], colname = 'merged_20_Aug', metadata.column='res.0.8') Let me know if that works. T Thanks! Em qua, 22 de ago de 2018 às 12:51, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Thanks. Here is the dimension, they are different, does this cause the error? How should I fix it? Thanks. ***@***.***) [1] 29408 4859 ***@***.***) [1] 4391 34 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqUR-EposuspnxbJ4-r66qqbfV79HaXks5uTYwHgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo,
Thanks. I tried and it still showed the same error...
Here is the code:

data <- as.data.frame(as.matrix([email protected][,rownames([email protected])]))
cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0)
[1] "Initializing CellRouter object"
dim(data)
[1] 29408 4391
dim([email protected])
[1] 4391 34
cellrouter <- addInfo(cellrouter, metadata = [email protected], colname = 'merged_20_Aug', metadata.column='res.0.8')
Error in rep(colors, times = replicate_row) : invalid 'times' argument
Best,
Kun

from cellrouter.

edroaldo commented on August 18, 2024

A previous user had the same issue and this worked for him:

data <- ***@***.***)) cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0,

+ min.genes=0) [1] "Initializing CellRouter object" *> metadata <- [email protected]*

cellrouter <- addInfo(cellrouter, metadata=metadata, colname = 'res.0.7', metadata.column = 'res.0.7')

Can you try to create a metadata variable as above and call addInfo as above? I know that this should be equivalent to what you are doing but I noticed that sometimes, I cannot save seurat@data. I need assign to seurat@data to a variable and then save the variable... It does not make too much sense but I am surprised you are getting this error. Other users, including myself, haev used results from seurat wihth cellrouter too... Pleas,e let me know if the code above works... Thanks! Em qua, 22 de ago de 2018 às 16:46, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Thanks. I tried and it still showed the same error... Here is the code: data <- ***@***.******@***.*** )])) cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, - min.genes=0) [1] "Initializing CellRouter object" dim(data) [1] 29408 4391 ***@***.***) [1] 4391 34 cellrouter <- addInfo(cellrouter, metadata = ***@***.***, colname = 'merged_20_Aug', metadata.column='res.0.8') Error in rep(colors, times = replicate_row) : invalid 'times' argument Best, Kun — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqUR8JM8hLbZaLsbD4fu6KVZrO8h6EWks5uTcMkgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo,
I tried to make the variable and called the addInfo, but met with the same error...
My Seurat object has many different annotation, need I delete some?
Best,
Kun

from cellrouter.

edroaldo commented on August 18, 2024

In principle, you would not need to delete any information. Can you please send me the follow info: [email protected][1:5,1:5] seurat@data[1:5,1:5] seurat@metadata[1:5,] Just want do double-check a few things.. Thanks! Em qua, 22 de ago de 2018 às 17:06, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, I tried to make the variable and called the addInfo, but met with the same error... My Seurat object has many different annotation, need I delete some? Best, Kun — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqURxBvTvmmIzDdOp8yNQN---ZKYemhks5uTcfLgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo,
Sorry for the delayed reply, just had a meeting.
Here is the info:

from cellrouter.

edroaldo commented on August 18, 2024

This is the issue: the column names in your [email protected] do not match with the rownames in [email protected]. In [email protected] there seems to be an additional "D" in front of your cell ids. I do not know how your importing your data into seurat but you need to manage to make the column names of you @raw.data object match with the row names in @meta.data. This is not a cellrouter issue. Hope it helps. Let me know if that works. Thanks! Em qua, 22 de ago de 2018 às 19:20, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Sorry for the delayed reply, just had a meeting. Here is the info: ***@***.***[1:5,1:5] 5 x 5 sparse Matrix of class "dgCMatrix" 2T_AAAGTAGAGAACAATC 2T_AACACGTGTTAAAGAC 2T_ACATCAGGTCTGGTCG 2T_ACGAGCCCAATCGGTT 2T_ACGGAGACAGCGTCCA RP11-34P13.7 . . . . . AL627309.1 . 1 . . . AP006222.2 . . 2 . . RP4-669L17.10 . . . . . RP11-206L10.3 . . . . 1 ***@***.***[1:5,1:5] 5 x 5 sparse Matrix of class "dgCMatrix" 2T_AAAGTAGAGAACAATC 2T_ACGAGCCCAATCGGTT 2T_AGGGAGTAGTGACATA 2T_CACACAACACTCGACG 2T_CAGTAACTCGCGCCAA RP11-34P13.7 . . . . . AL627309.1 . . . . . AP006222.2 . . . . 1.010743 RP4-669L17.10 . . . 1.273872 . RP11-206L10.3 . . . . . ***@***.***[1:5,] nGene nUMI orig.ident percent.mito batch res.0.6 res.0.4 res.0.8 res.1.2 infomap walktrap multilevel velocyto tree.ident newId D2T_AAAGTAGAGAACAATC 1650 2944 D2_T 0.2568213 D2T 0 3 1 6 11 8 6 2 NA preSPG D2T_ACGAGCCCAATCGGTT 1384 2517 D2_T 0.3313421 D2T 3 3 4 6 11 8 6 2 3 preSPG D2T_AGGGAGTAGTGACATA 1988 3387 D2_T 0.2320789 D2T 1 3 0 6 11 8 6 2 3 preSPG D2T_CACACAACACTCGACG 1900 3894 D2_T 0.3066426 D2T 3 3 4 6 11 8 6 2 3 preSPG D2T_CAGTAACTCGCGCCAA 2634 5734 D2_T 0.2133869 D2T 0 3 2 6 11 8 6 2 3 preSPG ID ident newID_monocle S.Score old.ident tempID newPGCLIDD source new_diffSPG GCnew monocle_ident 2T_AAAGTAGAGAACAATC PreSPG Intermediate Intermediate -0.11751679 Neonatal Intermediate PreSPG Neonatal 2T_ACGAGCCCAATCGGTT PreSPG Intermediate Intermediate -0.16908749 Neonatal Intermediate PreSPG Neonatal 2T_AGGGAGTAGTGACATA Intermediate Intermediate 0.07688675 Neonatal Intermediate PreSPG Neonatal 2T_CACACAACACTCGACG PreSPG Intermediate Intermediate 0.05150827 Neonatal Intermediate PreSPG Neonatal 2T_CAGTAACTCGCGCCAA PreSPG Intermediate Intermediate -0.14460912 Neonatal Intermediate PreSPG Neonatal Monocle_ident newcombinedID G2M.Score Phase platform var.ratio.pca merged_ID_12Aug gPGC_merged_20_Aug 2T_AAAGTAGAGAACAATC Intermediate preSPG -0.04297471 G1 10X 0.9234762 PreSPG PreSPG 2T_ACGAGCCCAATCGGTT Intermediate preSPG 0.09448125 G2M 10X 0.9433806 PreSPG PreSPG 2T_AGGGAGTAGTGACATA Intermediate preSPG -0.12927445 S 10X 0.7457309 PreSPG PreSPG 2T_CACACAACACTCGACG Intermediate preSPG 0.26457024 G2M 10X 0.9392665 PreSPG PreSPG 2T_CAGTAACTCGCGCCAA Intermediate preSPG -0.16218555 G1 10X 0.8728712 PreSPG PreSPG — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqUR7VI8PE2ZuO6UkvSpqb4nXxMdGwqks5uTecmgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

from cellrouter.

edroaldo commented on August 18, 2024

hum... that's strange, could you please send to me: cellrouter@rawdata[1:5,1:5] cellrouter@ndata[1:5,1:5] class([email protected]) Not sure what it is wrong on your end... so need more info... thanks! Em qua, 22 de ago de 2018 às 22:35, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Sorry, it's my fault. All these column names contain "D", I deleted it to keep them in one line. But left some... All other info are correct. So, I guess it's not because of this. Sorry about this. Can you check if there are any other issue? Thanks. Best,Kun — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqUR_Rrzs0qjqmmhL9mM7FlhtY3tmefks5uThTkgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo, I don't have the data on my laptop, will send it to you tomorrow. Best, Kun From: edroaldo [[email protected]] Sent: Wednesday, August 22, 2018 7:47 PM To: edroaldo/cellrouter Cc: Tan, Kun; Author Subject: Re: [edroaldo/cellrouter] cellrouter addInfo (#15) hum... that's strange, could you please send to me: cellrouter@rawdata[1:5,1:5] cellrouter@ndata[1:5,1:5] class([email protected]) Not sure what it is wrong on your end... so need more info... thanks! Em qua, 22 de ago de 2018 às 22:35, KunUCSD <[email protected]> escreveu:

…

-- Edroaldo — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#15 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AgAWC-3z2rJ7_ISQoy0Js_iXw4xbfnHtks5uThfXgaJpZM4WG15P>.

from cellrouter.

kunUCSD commented on August 18, 2024

Dear Edroaldo,
Sorry about the delayed reply, have so many things to handle today.
Here is the info:

cellrouter@rawdata[1:5,1:5]
D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA
RP11-34P13.7 0 0 0 0 0
AL627309.1 0 0 0 0 0
AP006222.2 0 0 0 0 1
RP4-669L17.10 0 0 0 1 0
RP11-206L10.3 0 0 0 0 0
cellrouter@ndata[1:5,1:5]
D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA
RP11-34P13.7 0 0 0 0 0
AL627309.1 0 0 0 0 0
AP006222.2 0 0 0 0 1
RP4-669L17.10 0 0 0 1 0
RP11-206L10.3 0 0 0 0 0
class([email protected])
[1] "data.frame"

Best,
Kun

from cellrouter.

edroaldo commented on August 18, 2024

Hi, I am sorry but I cannot reproduce your error. I get the same error as you if dimensions are different. I have a seurat analysis froma previous project that I just loaded into my R section and used the seurat clusters that I previously identified and everything worked. Are sure you are not missing anything? This code worked just find for me: data <- as.data.frame(as.matrix([email protected])) data <- data[,rownames([email protected])] cellrouter <- CellRouter(rawdata=as.data.frame(data), min.cells=0, min.genes=0) cellrouter <- addInfo(cellrouter, metadata = [email protected], colname = 'seurat', metadata.column = 'res.0.6') Thanks! Em sex, 24 de ago de 2018 às 00:09, KunUCSD <[email protected]> escreveu:

…

Dear Edroaldo, Sorry about the delayed reply, have so many things to handle today. Here is the info: ***@***.***[1:5,1:5] D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA RP11-34P13.7 0 0 0 0 0 AL627309.1 0 0 0 0 0 AP006222.2 0 0 0 0 1 RP4-669L17.10 0 0 0 1 0 RP11-206L10.3 0 0 0 0 0 ***@***.***[1:5,1:5] D2T_AAAGTAGAGAACAATC D2T_ACGAGCCCAATCGGTT D2T_AGGGAGTAGTGACATA D2T_CACACAACACTCGACG D2T_CAGTAACTCGCGCCAA RP11-34P13.7 0 0 0 0 0 AL627309.1 0 0 0 0 0 AP006222.2 0 0 0 0 1 RP4-669L17.10 0 0 0 1 0 RP11-206L10.3 0 0 0 0 0 ***@***.***) [1] "data.frame" Best, Kun — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJqURxpHiJ_r-_R4C3IAbtynvVvsl5Ihks5uT3ySgaJpZM4WG15P> .

-- Edroaldo

from cellrouter.

kunUCSD commented on August 18, 2024

Thank you Edroaldo for all efforts, I'll re-make the object, and see if it works.
Thanks,
Kun

from cellrouter.

cellrouter addInfo about cellrouter HOT 15 OPEN

Comments (15)

Related Issues (20)

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent