Error in as.igraph.vs(graph, from) : Invalid vertex names

[mitchTwoTimes]

Hi,

Can you please help me understand what is required for get_tf_network? I don't understand why there would be an issue plotting if there are plenty of TF:Target interactions in my GRN.

> grnTF <- 'RFX3'
> glm_network@meta[glm_network@meta$tf == grnTF,]
# A tibble: 87 × 9
# Groups:   target, tf [87]
   tf    target   estimate n_regions n_genes n_tfs regions                                                                                                                pval     padj
   <chr> <chr>       <dbl>     <int>   <int> <int> <chr>                                                                                                                 <dbl>    <dbl>
 1 RFX3  ABCA1     -0.339         58      87    62 chr9-103942767-103943002;chr9-105313283-105313329;chr9-105329432-105329519                                         7.88e- 6 1.16e- 4
 2 RFX3  ADAMTS9    0.0214        50      87    42 chr3-63688014-63688078                                                                                             1.68e- 6 2.87e- 5
 3 RFX3  ADGRV1     0.478         70      87    77 chr5-89498890-89498912;chr5-90017336-90017531;chr5-90548195-90548407;chr5-91730137-91730363;chr5-91875156-91875250 9.23e- 6 1.34e- 4
 4 RFX3  AGBL4     -0.0201        61      87    31 chr1-47804255-47804358                                                                                             3.19e- 3 2.12e- 2
 5 RFX3  ANLN      -0.0394        70      87    73 chr7-36037473-36037546;chr7-36986510-36986722                                                                      5.32e- 3 3.20e- 2
 6 RFX3  ARHGAP22   0.0415        48      87    56 chr10-48739519-48739802                                                                                            2.06e- 2 9.19e- 2
 7 RFX3  ASIC2      0.0408        83      87    43 chr17-34077521-34077548                                                                                            5.50e- 3 3.29e- 2
 8 RFX3  CASC15     0.0750       108      87    93 chr6-22036459-22036589;chr6-22098791-22098890                                                                      8.29e-18 5.00e-16
 9 RFX3  CBLB       0.218         45      87    37 chr3-104992925-104992945                                                                                           6.34e-14 2.83e-12
10 RFX3  CCSER1     0.326         61      87    69 chr4-90542414-90542465                                                                                             1.29e- 5 1.81e- 4
# … with 77 more rows

> proj <- get_tf_network(proj, network = "glm_network",  tf = grnTF)
Getting shortest paths from TF
Error in as.igraph.vs(graph, from) : Invalid vertex names

> traceback()
5: stop("Invalid vertex names")
4: as.igraph.vs(graph, from)
3: igraph::all_shortest_paths(gene_graph, tf, features, mode = "out")
2: get_tf_network.SeuratPlus(proj, network = "glm_network", tf = grnTF)
1: get_tf_network(proj, network = "glm_network", tf = grnTF)

Thank you

[GouQiao]

Hi,

Can you please help me understand what is required for get_tf_network? I don't understand why there would be an issue plotting if there are plenty of TF:Target interactions in my GRN.

> grnTF <- 'RFX3'
> glm_network@meta[glm_network@meta$tf == grnTF,]
# A tibble: 87 × 9
# Groups:   target, tf [87]
   tf    target   estimate n_regions n_genes n_tfs regions                                                                                                                pval     padj
   <chr> <chr>       <dbl>     <int>   <int> <int> <chr>                                                                                                                 <dbl>    <dbl>
 1 RFX3  ABCA1     -0.339         58      87    62 chr9-103942767-103943002;chr9-105313283-105313329;chr9-105329432-105329519                                         7.88e- 6 1.16e- 4
 2 RFX3  ADAMTS9    0.0214        50      87    42 chr3-63688014-63688078                                                                                             1.68e- 6 2.87e- 5
 3 RFX3  ADGRV1     0.478         70      87    77 chr5-89498890-89498912;chr5-90017336-90017531;chr5-90548195-90548407;chr5-91730137-91730363;chr5-91875156-91875250 9.23e- 6 1.34e- 4
 4 RFX3  AGBL4     -0.0201        61      87    31 chr1-47804255-47804358                                                                                             3.19e- 3 2.12e- 2
 5 RFX3  ANLN      -0.0394        70      87    73 chr7-36037473-36037546;chr7-36986510-36986722                                                                      5.32e- 3 3.20e- 2
 6 RFX3  ARHGAP22   0.0415        48      87    56 chr10-48739519-48739802                                                                                            2.06e- 2 9.19e- 2
 7 RFX3  ASIC2      0.0408        83      87    43 chr17-34077521-34077548                                                                                            5.50e- 3 3.29e- 2
 8 RFX3  CASC15     0.0750       108      87    93 chr6-22036459-22036589;chr6-22098791-22098890                                                                      8.29e-18 5.00e-16
 9 RFX3  CBLB       0.218         45      87    37 chr3-104992925-104992945                                                                                           6.34e-14 2.83e-12
10 RFX3  CCSER1     0.326         61      87    69 chr4-90542414-90542465                                                                                             1.29e- 5 1.81e- 4
# … with 77 more rows

> proj <- get_tf_network(proj, network = "glm_network",  tf = grnTF)
Getting shortest paths from TF
Error in as.igraph.vs(graph, from) : Invalid vertex names

> traceback()
5: stop("Invalid vertex names")
4: as.igraph.vs(graph, from)
3: igraph::all_shortest_paths(gene_graph, tf, features, mode = "out")
2: get_tf_network.SeuratPlus(proj, network = "glm_network", tf = grnTF)
1: get_tf_network(proj, network = "glm_network", tf = grnTF)

Thank you

Hey, I also met the same error as you did.
Did you find solutions?

[joschif]

It's possible that this is because the graph is disconnected and certain nodes cannot be reached from a TF. I'll see if I can fix this to through a warning rather than an error