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quadbio / Pando

Multiome GRN inference.
https://quadbio.github.io/Pando/
MIT License
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Error in as.igraph.vs(graph, from) : Invalid vertex names #32

Open mitchTwoTimes opened 1 year ago

mitchTwoTimes commented 1 year ago

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 commented 11 months ago

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 commented 11 months ago

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