what is the "condition" in orderCells() function

[lizhaozhi]

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"

[wwh199459]

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]

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

[honghh2018]

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

Best

[honghh2018]

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

[yishan03]

The same issue here. @ctrapnell

[honghh2018]

您好！已经收到邮件，祝好！                                    洪汉辉

[44REAM]

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]

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]

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

[MwGuo11]

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]

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:

1. download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/
2. decompress the package 'monocle_2.24.0.tar.gz', and get a 'monocle' folder.
3. 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)

4. save the 'order_cell.R' file.
5. copy the 'monocle' folder and paste to the location where I usually install my packages.
6. 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]

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:

1. download monocle from https://www.bioconductor.org/packages/3.15/bioc/src/contrib/Archive/monocle/
2. decompress the package 'monocle_2.24.0.tar.gz', and get a 'monocle' folder.
3. 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)

4. save the 'order_cell.R' file.
5. copy the 'monocle' folder and paste to the location where I usually install my packages.
6. 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]

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]

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]

@weu74lin

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

[patrickeboada]

@weu74lin great idea!

[yejingyu0628]

@weu74lin @44REAM Thanks very much！

[orange511]

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?

[cieloLab]

@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]

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"))

[cieloLab]

@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]

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.

[cieloLab]

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

[Georgeguoql]

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]

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]

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]

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]

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]

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]

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.