processtrajectories error
Opened this issue · 1 comments
Hello, I seem to be getting the same error as "processtrajectories error #9" however I am following the Paul example using that data and copy pasting the the exact script from the tutorial. All seemed to be going quite well until this step. Please advise, thanks so much.
Here is the command and output I am seeing:
cellrouter <- processTrajectories(cellrouter, rownames(cellrouter@ndata), path.rank=ranks[3], num.cells = 3, neighs = 3,column.ann = 'population', column.color = 'colors')
[1] "parsing trajectory information"
[1] 3
Error in igraph::induced.subgraph(graph = g, vids = unlist(igraph::neighborhood(graph = g, :
Not a graph object
here is some other info I noticed you requested in the other thread:
user@server:~$ ls results
custom_1.pdf pathsCells_FlowNetwork_paths.ser
heatmap_all_genes_CellRouter_clusters.png PCA_1.pdf
heatmap_top_10_genes_CellRouter_clusters.png PCA_2.pdf
heatmap_top_10_genes_original_clusters.png tSNE_1.pdf
heatmap_top_10_genes_sorted_populations.png tSNE_2.pdf
knn_tsne_CellRouter_clusters.pdf tSNE_graphClustering_clusters.pdf
paths tSNE_original_clusters.pdf
user@server:~$ ls results/paths
6.1 6.2 6.3 6.4 6.5 6.7 6.8 6.9 cell_edge_weighted_network.txt
user@server:~$ java -version
openjdk version "11.0.7" 2020-04-14
OpenJDK Runtime Environment (build 11.0.7+10-post-Ubuntu-2ubuntu218.04)
OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Ubuntu-2ubuntu218.04, mixed mode, sharing)
user@server:~$ ls results/paths/6.1
CellRouter.sh Cells_FlowNetwork_scripts.R
Cells_FlowNetwork_all_paths_subnet_exportGML.R Cells_FlowNetwork_scripts.Rout
Cells_FlowNetwork_all_paths_subnet.txt cell_sinks.txt
Cells_FlowNetwork_all_paths_totalFlow.txt cell_sources.txt
Cells_FlowNetwork_all_paths.txt
then I found in the Cells_FlowNetwork_scripts.Rout file that it was stalling when attempting to load igraph:
library(igraph);
Error in library(igraph) : there is no package called ‘igraph’
Execution halted
this is because I have separate Rlibs directories on this server and so it needed to load my libPaths() first. I added that line to the CellRouter_Class.R script:
setMethod("processTrajectories",
signature="CellRouter",
definition=function(object, genes, path.rank, num.cells, neighs, column.ann, column.color){
.libPaths(c("wsRlibs361", .libPaths()))
library(igraph)
object@gene.trajectory <- genes
and it fixed that problem? but introduced what seems to be a worse one at this earlier step:
cellrouter <- findPaths(cellrouter, column='population', libdir, paste(getwd(), 'results/paths', sep='/'), method="graph")
-------------------Transition: 6.1 -----------------------
- Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.2 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.3 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.4 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.5 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.7 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.8 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.9 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
-------------------Transition: 6.10 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
I thought it was a server related problem however I also tried the same wokflow on my macbook and at the same step got this
cellrouter <- findPaths(cellrouter, column='population', libdir, paste(getwd(), 'results/paths', sep='/'), method="graph")
-------------------Transition: 6.1 -----------------------
- Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
-------------------Transition: 6.2 ----------------------- - Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Now I am totally lost. Please let me know if there is anything else that would help get to the bottom of this. Thanks again.
W
so after seeing another post, on the macbook I changed
libdir <- "CellRouter"
to
libdir <- "~/CellRouter"
and it seemed to work properly
cellrouter <- findPaths(cellrouter, column='population', libdir, paste(getwd(), 'results/paths', sep='/'), method="graph")
-------------------Transition: 6.1 -----------------------
- Computing flow network
Creating flow network...
Number of sources: 1
Number of sinks: 1
Network size before: 2699
New source s added
New target t added
Network size: 2701
Computing flow
Number of paths: 10
Number of paths: 20
Number of paths: 30
Number of paths: 40
Number of paths: 50
Number of paths: 60
Number of paths: 70
Number of paths: 80
Number of paths: 90
Number of paths: 100
Number of paths: 110
Number of paths: 120
Number of paths: 130
Number of paths: 140
path size before: 145
path size after: 145
Subnet size: 141
merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R
-------------------Transition: 6.2 ----------------------- - Computing flow network
...
then I get to here and:
cellrouter <- processTrajectories(cellrouter, rownames(cellrouter@ndata), path.rank=ranks[3], num.cells = 3, neighs = 3,column.ann = 'population', column.color = 'colors')
[1] "parsing trajectory information"
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths_subnet.gml
[1] 3
[1] "6.1"
[1] "6.2"
[1] "6.3"
[1] "6.4"
[1] "6.5"
[1] "6.7"
[1] "6.8"
[1] "6.9"
names <- unique(names(cellrouter@pathsinfo$distr))
cellrouter <- correlationPseudotime(cellrouter, type='spearman')
[1] "computing correlation with the pseudotime"
6.1
6.2
6.3
6.4
6.5
6.7
6.8
6.9
cellrouter <- topGenes(cellrouter, 0.8, 0.1)
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
'x' must be atomic
stuck again :(