what is the "condition" in orderCells() function #434

lizhaozhi · 2020-10-07T21:37:18Z

Hi,

I am trying to construct single-cell trajectories using monocle, but I got an error message when I use the orderCells() function.
the condition has length > 1 and only the first element will be used

any ideas what's going on? Appreciate your ideas.

Maybe it is caused by one if() statement in project2MST() function.
The class of this projection matrix in this project2MST() function is c("matrix", "array").

  projection <- rbind(projection, tmp)        -> "matrix", "array"
  if(class(projection) != 'matrix')                 -> error
    projection <- as.matrix(projection)

possible solution:
projection <- as.matrix(rbind(projection, tmp))

version:
R Biobase eSet ExpressionSet CellDataSet
"4.0.0" "2.48.0" "1.3.0" "1.0.0" "1.2.0"

The text was updated successfully, but these errors were encountered:

wwh199459 · 2022-05-30T01:20:10Z

I have the same problem, did you solve it? Error in if (class(projection) != "matrix") projection <- as.matrix(projection) :
the condition has length > 1
此外: Warning message:
In graph.dfs(dp_mst, root = root_cell, neimode = "all", unreachable = FALSE, :
Argument neimode' is deprecated; use mode' instead

wangshisheng · 2022-06-06T14:13:29Z

I have the same problem, too. Anyone could help? Many thanks. Bests.

honghh2018 · 2022-06-09T11:14:38Z

@wangshisheng @ctrapnell @lizhaozhi
i had the same issue, had anyone could help us?
my R version was 4.2.0

Best

honghh2018 · 2022-06-10T01:37:32Z

Had any advice for this issue ? @wangshisheng @ctrapnell @lizhaozhi
Many thanks,
Best

yishan03 · 2022-06-12T20:11:52Z

The same issue here. @ctrapnell

honghh2018 · 2022-06-12T20:12:09Z

您好！已经收到邮件，祝好！洪汉辉

44REAM · 2022-06-16T17:28:45Z

I have the same problem, this is my solution.
I download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/
And change the code in function project2MST() in order_cell.R file.

from

if(class(projection) != 'matrix')                 
    projection <- as.matrix(projection)

to

projection <- as.matrix(projection)

then install the package using install.packages("path to folder with the package", repos = NULL, type = "source")

hope this help

lyuguol · 2022-06-17T08:20:05Z

I have the same problem, this is my solution. I download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/ And change the code in function project2MST() in order_cell.R file.

from
if(class(projection) != 'matrix')                 
    projection <- as.matrix(projection)
to
projection <- as.matrix(projection)
then install the package using install.packages("path to folder with the package", repos = NULL, type = "source")

hope this help

Dear 44REAM,
Thank you. After changing the function, did you make a new archived packaged with 'tar -czf monocle_2.24.0.tar.gz monocle 2' to replace the original one and installed? or you installed the package with the unarchived folder containing the modified 'order_cell.R' 'install.packages("R_package/monocle 2", repos = NULL, type = "source")'?
I encountered the problem in installation....Could you show me more details about how you performed the installation?
Many thanks!
Guoliang

MwGuo11 · 2022-06-18T12:15:02Z

I have the same problem, too. Anyone could help? Thanks very much. Bests.

MwGuo11 · 2022-06-18T12:15:54Z

您好！已经收到邮件，祝好！洪汉辉

您好，您的问题解决了吗，谢谢！

lyuguol · 2022-06-19T17:34:05Z

Dear Hanhui,

Yes, the problem was perfectly solved by following 44REAM's solution, however, with a bit of modification when performing the last step of installation.

I quote the following solution again as a big thanks for 44REAM as well:

download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/
decompress the package 'monocle_2.24.0.tar.gz', and get a 'monocle' folder.
open the folder 'monocle/R', change the code in function 'project2MST()' in the 'order_cell.R' file:
change from

if(class(projection) != 'matrix')
projection <- as.matrix(projection)

to

projection <- as.matrix(projection)

save the 'order_cell.R' file.
copy the 'monocle' folder and paste to the location where I usually install my packages.
In R studio, using the command to load the 'monocle' folder:

devtools::load_all("path to the location/monocle")

7.Done. and managed to run the 'orderCells(cds)'.

Thank you and best,

Guoliang

MwGuo11 · 2022-06-20T02:35:58Z

Dear Hanhui,

Yes, the problem was perfectly solved by following 44REAM's solution, however, with a bit of modification when performing the last step of installation.

I quote the following solution again as a big thanks for 44REAM as well:

download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/

decompress the package 'monocle_2.24.0.tar.gz', and get a 'monocle' folder.

open the folder 'monocle/R', change the code in function 'project2MST()' in the 'order_cell.R' file:
change from

if(class(projection) != 'matrix') projection <- as.matrix(projection)

to

projection <- as.matrix(projection)

save the 'order_cell.R' file.

copy the 'monocle' folder and paste to the location where I usually install my packages.

In R studio, using the command to load the 'monocle' folder:

devtools::load_all("path to the location/monocle")

7.Done. and managed to run the 'orderCells(cds)'.

Thank you and best,

Guoliang

Thanks very much！

patrickeboada · 2022-06-21T17:40:57Z

Thank you @MwGuo11 & @44REAM for providing the edit to update the package.

I noticed that I could not rerun my monocle2 pipeline on the same data that I produced results from previously. It may be from updating my R to the latest version.

Now that I've utilized your update I can get past orderCells(). However, I cannot get retrieve BEAM() results.

`BEAM_res <- BEAM(monocle_cds, branch_point = 1, cores = 8)

Error in if (progenitor_method == "duplicate") { :
the condition has length > 1`

I never returned this error before for BEAM(). Does anyone have any experience or input on this error?

weu74lin · 2022-06-23T03:45:11Z

Thank you @MwGuo11 & @44REAM for providing the edit to update the package.

I noticed that I could not rerun my monocle2 pipeline on the same data that I produced results from previously. It may be from updating my R to the latest version.

Now that I've utilized your update I can get past orderCells(). However, I cannot get retrieve BEAM() results.

`BEAM_res <- BEAM(monocle_cds, branch_point = 1, cores = 8)

Error in if (progenitor_method == "duplicate") { : the condition has length > 1`

I never returned this error before for BEAM(). Does anyone have any experience or input on this error?

I also have the same problem, I modified the code of / monocle/R /BEAM.R on the basis of 44REAM's solution.

from:

if (progenitor_method == "duplicate") { }
else if (progenitor_method == "sequential_split") { }

to:

if ('duplicate' %in% progenitor_method){}
else if('sequential_split' %in% progenitor_method){}

patrickeboada · 2022-06-23T09:14:56Z

@weu74lin

Thank you for your advice on these edits.
This change corrected the error.

patrickeboada · 2022-06-23T10:15:48Z

@weu74lin great idea!

yejingyu0628 · 2022-07-12T09:47:30Z

@weu74lin @44REAM Thanks very much！

orange511 · 2022-08-15T14:04:43Z

Hi, I cannot get retrieve plot_genes_branched_heatmap() results.

plot_genes_branched_heatmap(mycds_sub_beam,
branch_point = 1,
num_clusters = 2,
show_rownames = T)

Error in if (isSparseMatrix(exprs(X))) { : the condition has length > 1
In addition: Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'

Does anyone have any experience or input on this error?

hereFadeStar · 2022-11-10T17:38:04Z

@orange511
it happened to me once when i set the parameter 'cores = 1' in this function. if you change to 2 or else, it will pass; if this doesn't work, you should find another solution.

zy-fang · 2022-11-11T03:38:23Z

Hi, I cannot get retrieve plot_genes_branched_heatmap() results.

plot_genes_branched_heatmap(mycds_sub_beam, branch_point = 1, num_clusters = 2, show_rownames = T)

Error in if (isSparseMatrix(exprs(X))) { : the condition has length > 1 In addition: Warning message: In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE : 'length(x) = 2 > 1' in coercion to 'logical(1)'

Does anyone have any experience or input on this error?

I met the same problem.

I modified the code of / monocle/R /utils.R
from:
class(x) %in% c("dgCMatrix", "dgTMatrix")
to:
any(class(x) %in% c("dgCMatrix", "dgTMatrix"))

hereFadeStar · 2022-11-11T15:32:36Z

@zy-fang
thank you! it works after i modified that. And it fix the same error when i use plot_genes_branched_pseudotime. however, i still got some warning:

plot_genes_branched_heatmap(cds[row.names(subset(BEAM_res, qval < 1e-4)),],  branch_point = 1,  num_clusters = 4, 
                                   cores = 4,use_gene_short_name = T,  show_rownames = T)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE : 'length(x) = 2 > 1' in coercion to 'logical(1)'

plot_genes_branched_pseudotime(cds[genes,], branch_point = 1, color_by = "State")
Warning messages:
1: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 6 (<-localhost:11964)
2: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 5 (<-localhost:11964)
3: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 4 (<-localhost:11964)
4: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 3 (<-localhost:11964)
5: In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

Did these warning happen to you and should i ignore it? thank you very much!

zy-fang · 2022-11-12T12:25:47Z

I think these warnings can be ignored.

In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'.

This is because when cellData is a matrix, class(cellData) is going to be c("matrix", "array"). So the class(cellData) != "matrix" will be c(FALSE,TRUE). When do the “&&”at the end, only the first one (FALSE) is taken into account.

4: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) - :
closing unused connection 3 (<-localhost:11964)

This warning is about multiple core parallelism.

hereFadeStar · 2022-11-13T06:28:32Z

@zy-fang
Thank you for your advice and these details which help me a lot.

Georgeguoql · 2022-11-21T16:07:05Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:06Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:07Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:07Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:08Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:08Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:08Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:08Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:08Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:09Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

Georgeguoql · 2022-11-21T16:07:09Z

sc_cds <- newCellDataSet(

as.matrix(ct),
phenoData = pd,
featureData =fd,
expressionFamily = negbinomial.size(),
lowerDetectionLimit=1)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
'length(x) = 2 > 1' in coercion to 'logical(1)'
I also meet this warnings when using the newCellDataSet function.
Furthermore, when I run the following codes
cds <- estimateSizeFactors(cds)
Error in if (isSparseMatrix(counts)) { : the condition has length > 1

cds <- estimateDispersions(cds)
Error in .local(object, ...) :
NAs found in size factors. Have you called 'estimateSizeFactors'?
These error have made the analysis discontinued in the following steps.
Thank you for anyone who can solve these problems.

vailin1992 · 2022-12-01T16:29:15Z

I attach a modified version of Monocle (2.26.0) according to the discussion. One can install it locally. I hope this one helps somebody.
monocle_2.26.0.tar.gz

jehan-uhn · 2022-12-19T20:00:03Z

I attach a modified version of Monocle (2.26.0) according to the discussion. One can install it locally. I hope this one helps somebody. monocle_2.26.0.tar.gz

You have my eternal gratitude, this was the most perfectly helpful thing it solved my issue with EstimateSizeFactors immediately.

cole-trapnell-lab/monocle-release#434

Georgeguoql · 2022-12-30T04:49:34Z

Thank you all the guys! I have also updated the latest modifications which have changed the Beam.R code, which will help the monocle2 work well.
monocle_2.26.0.tar.gz

ZivTQ · 2023-03-10T09:39:23Z

I attach a modified version of Monocle (2.26.0) according to the discussion. One can install it locally. I hope this one helps somebody. monocle_2.26.0.tar.gz

Hi, have you accept this error in ordercell?:error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/rinlinedfuns.h:537

fpengstudy · 2023-03-14T10:58:30Z

@ZivTQ
Hi, I met the same error, and I saw this problem in other issues in #138 .
I am trying to use monocle3 for my 50k cells. Have you fixed this problem yet?

ZivTQ · 2023-03-15T00:40:37Z

Hi The error has not been solved. Monocle3 is alright. I am trying to debug,......if successed, I will contact with you! best wishes | NameTAN Qiang ***@***.*** Organization: Address：Zhejiang university，Hangzhou，China Telephone: 手机：18883394145 | 扫描该二维码，可以将电子名片迅速保存到手机使用帮助 | At 2023-03-14 18:58:43, "fpengstudy" ***@***.***> wrote: @ZivTQ Hi, I met the same error, and I saw this problem in other issues in #138 . I am trying to use monocle3 for my 50k cells. Have you fixed this problem yet? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

zr0719 · 2023-04-10T01:26:56Z

I attach a modified version of Monocle (2.26.0) according to the discussion. One can install it locally. I hope this one helps somebody. monocle_2.26.0.tar.gz

Thanks you so much!

zr0719 · 2023-04-10T07:42:11Z

@zy-fang thank you! it works after i modified that. And it fix the same error when i use plot_genes_branched_pseudotime. however, i still got some warning:

plot_genes_branched_heatmap(cds[row.names(subset(BEAM_res, qval < 1e-4)),],  branch_point = 1,  num_clusters = 4, 
                                   cores = 4,use_gene_short_name = T,  show_rownames = T)
Warning message:
In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE : 'length(x) = 2 > 1' in coercion to 'logical(1)'

plot_genes_branched_pseudotime(cds[genes,], branch_point = 1, color_by = "State")
Warning messages:
1: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 6 (<-localhost:11964)
2: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 5 (<-localhost:11964)
3: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 4 (<-localhost:11964)
4: In for (i in seq_len(differences)) r <- r[i1] - r[-length(r):-(length(r) -  :
  closing unused connection 3 (<-localhost:11964)
5: In class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE :
  'length(x) = 2 > 1' in coercion to 'logical(1)'

Did these warning happen to you and should i ignore it? thank you very much!
I met the same error when I run with HSMM[1:10,], but it turns to plot when I run with HSMM[c(1:5, 20:100),]. It's weird and I don't know why.

XiongYuZhang · 2023-05-16T19:35:01Z

I have the same problem, did you solve it? Error in if (class(projection) != "matrix") projection <- as.matrix(projection) : the condition has length > 1 此外: Warning message: In graph.dfs(dp_mst, root = root_cell, neimode = "all", unreachable = FALSE, : Argument neimode' is deprecated; use mode' instead

I also meet this error, I don't

I have the same problem, did you solve it? Error in if (class(projection) != "matrix") projection <- as.matrix(projection) : the condition has length > 1 此外: Warning message: In graph.dfs(dp_mst, root = root_cell, neimode = "all", unreachable = FALSE, : Argument neimode' is deprecated; use mode' instead

XiongYuZhang · 2023-05-16T20:10:28Z

How to modify the function projection2MST()? I can't find the codes of projection2MST function. I have download the monocle and found the orderCells and projection2MST(), but i can't find the raw codes of projection2MST.

weu74lin · 2023-05-17T06:52:36Z

How to modify the function projection2MST()? I can't find the codes of projection2MST function. I have download the monocle and found the orderCells and projection2MST(), but i can't find the raw codes of projection2MST.

You might want to unzip monocle_2.26.0.tar.gz, then look for orderCell.R in the monocle/R file and open modify projection2MST(), then re-zip the installation

XiongYuZhang · 2023-05-17T18:10:47Z

thank you so much for answering my questions

…

________________________________ From: weu74lin ***@***.***> Sent: Wednesday, May 17, 2023 14:52 To: cole-trapnell-lab/monocle-release ***@***.***> Cc: Xiong, Xingliang ***@***.***>; Comment ***@***.***> Subject: [EXTERNAL] Re: [cole-trapnell-lab/monocle-release] what is the "condition" in orderCells() function (#434) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> How to modify the function projection2MST()? I can't find the codes of projection2MST function. I have download the monocle and found the orderCells and projection2MST(), but i can't find the raw codes of projection2MST. You might want to unzip monocle_2.26.0.tar.gz, then look for orderCell.R in the monocle/R file and open modify projection2MST(), then re-zip the installation — Reply to this email directly, view it on GitHub<#434 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A2YARCCYTNWVW4C3JF2TVWTXGRYUDANCNFSM4SH56MGQ>. You are receiving this because you commented.Message ID: ***@***.***>

honghh2018 · 2023-10-18T11:08:13Z

thanks the @Georgeguoql, and in this step, i also modified the BEAM error
This was correct all above error package
hope it help
monocle_2.26.0.tar.gz

boyaisagirl · 2023-11-10T11:21:48Z

But I still meet the error when I run

beam_res <- BEAM(mycds[order.genes,], branch_point = 1, cores = 16)
Error in if (progenitor_method == "duplicate") { :
the condition has length > 1

Thank you all the guys! I have also updated the latest modifications which have changed the Beam.R code, which will help the monocle2 work well. monocle_2.26.0.tar.gz

01010101110 · 2023-12-03T13:59:52Z

I attach a modified version of Monocle (2.26.0) according to the discussion. One can install it locally. I hope this one helps somebody. monocle_2.26.0.tar.gz

Thank you so much!! It help to the error which bothers me for such a long time !!!

GWBHX-JJ · 2024-01-10T01:55:34Z

trace('project2MST', edit = T, where = asNamespace("monocle")) 运行此句代码
然后
在弹出窗口中把 if (elass(projection) != "matrix") 注释，并保存，重新运行即可
这个问题是这个包遗留的历史问题，因为包的创作者更新包的速度太快了

z-bluesky · 2024-03-16T10:39:00Z

orderCells(HSMM_myo)
Error in if (class(projection) != "matrix") projection <- as.matrix(projection) :
the condition has length > 1
In addition: Warning message:
In graph.dfs(dp_mst, root = root_cell, neimode = "all", unreachable = FALSE, :
Argument neimode' is deprecated; use mode' instead
I also encountered the same problem, I uninstalled it and then installed v2.30 and solved it

ixxmu mentioned this issue Sep 22, 2022

解决monocle中orderCells报错的一波三折 ixxmu/mp_duty#2762

Closed

zy-fang mentioned this issue Nov 11, 2022

plot_genes_branched_pseudotime and beam not working #472

Open

cpdong added a commit to cpdong/public that referenced this issue Dec 27, 2022

fix monocle2-DDRTree orderCells() function

8064346

cole-trapnell-lab/monocle-release#434

gebdu mentioned this issue Apr 27, 2023

Monocle2 orderCells error: the condition has length > 1 cole-trapnell-lab/monocle2-rge-paper#9

Closed

ixxmu mentioned this issue May 7, 2023

哪怕是在Linux服务器也可以解决monocle2的orderCells报错 ixxmu/mp_duty#3404

Closed

what is the "condition" in orderCells() function #434

what is the "condition" in orderCells() function #434

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patrickeboada commented Jun 21, 2022 •

edited

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edited