Error in matrix(sc_obj[[pseudotime_ID]], dimnames = list(colnames(sc_obj)

[Jylab-Genetics]

WT_1_tree <- nodePseudotime(TRO, "Pseudotime", "celltypes_Abbreviation", 50)
Error in matrix(sc_obj[[pseudotime_ID]], dimnames = list(colnames(sc_obj), :
length of 'dimnames' [1] not equal to array extent

colnames([email protected])
[1] "sample" "nUMI"
[3] "nGene" "celltypes_Abbreviation1"
[5] "celltypes_Abbreviation2" "origin"
[7] "celltype_lineage" "celltypes_Abbreviation"
[9] "log10GenesPerUMI" "RNA_snn_res.1"
[11] "seurat_clusters" "integrated_snn_res.1"
[13] "subclass2.1" "subclass2"
[15] "subclass1.1" "subclass1"
[17] "celltype2" "celltype"
[19] "nCount_RNA" "nFeature_RNA"
[21] "Size_Factor" "num_genes_expressed"
[23] "Pseudotime" "State"
[25] "cell_type"

[Jylab-Genetics]

path_tragedy <- bootstrap_pathfind(sequence_1 = as.matrix(WT_1_node_exp_mtx), sequence_2 = as.matrix(WT_2_node_exp_mtx)
, similarity_method= "spearman", threshold_method = "mean")
[1] 1 50
[1] 14 16
[1] 50 3
[1] 1 50
[1] 14 17
[1] 50 4
[1] 1 50
[1] 14 18
[1] 50 5
[1] 1 50
[1] 14 19
[1] 50 6
[1] 1 50
[1] 15 16
[1] 50 2
[1] 1 50
[1] 15 17
[1] 50 3
[1] 1 50
[1] 15 18
[1] 50 4
[1] 1 50
[1] 15 19
[1] 50 5
[1] 1 50
[1] 16 16
Error in dis_matrix[, -which(colnames(dis_matrix) %in% colnames(exp_mtx2))] :
incorrect number of dimensions

[No2Ross]

Hi,

Could I get some more info about the analysis setup and also what the output of dis_mtx_calculator is?

Also is the first error you posted still an issue or is it now fixed?

Best wishes,
Ross

[Jylab-Genetics]

Thank you very much for your prompt reply. The first issue has been resolved, but the second issue still exists

[Jylab-Genetics]

path_tragedy <- bootstrap_pathfind(sequence_1 = as.matrix(WT_1_node_exp_mtx), sequence_2 = as.matrix(WT_2_node_exp_mtx)
, similarity_method= "spearman", threshold_method = "mean")
Error in if (end_index_choice == 1) { : the condition has length > 1
dim(WT_2_node_exp_mtx )
[1] 8261 50
dim(WT_1_node_exp_mtx )
[1] 8261 50

[Jylab-Genetics]

path_tragedy <- bootstrap_pathfind(sequence_1 = as.matrix(WT_1_node_exp_mtx), sequence_2 = as.matrix(WT_2_node_exp_mtx)
, similarity_method= "spearman", threshold_method = "mean")
Error in if (end_index_choice == 1) { : the condition has length > 1
dim(WT_2_node_exp_mtx )
[1] 8261 50
dim(WT_1_node_exp_mtx )
[1] 8261 50

“We chose 50 interpolated points for our analysis and we wanted the window size to mean adjacent interpolated points had mixes of cells being considered." What is the basis for selecting this parameter, and how should I choose the appropriate value based on my data

[Jylab-Genetics]

path_tragedy <- bootstrap_pathfind(sequence_1 = as.matrix(WT_1_node_exp_mtx), sequence_2 = as.matrix(WT_2_node_exp_mtx)
, similarity_method= "spearman", threshold_method = "mean")
Error in if (end_index_choice == 1) { : the condition has length > 1
dim(WT_2_node_exp_mtx )
[1] 8261 50
dim(WT_1_node_exp_mtx )
[1] 8261 50

“We chose 50 interpolated points for our analysis and we wanted the window size to mean adjacent interpolated points had mixes of cells being considered." What is the basis for selecting this parameter, and how should I choose the appropriate value based on my data
When I choose different values, I report different errors

[No2Ross]

We use the number of clusters in the dataset as a proxy for number of interpolated points, around 10-20 interpolated points per cluster in the dataset.

I've been fixing some bugs and some issues with how we get the expression values of the interpolated points. Will commit them just now. If you redownload the TrAGEDy file after this, hopefully this will fix the issue. If not, please let me know!