fix: Fail if "layout" attribute doesn't match the number of vertices
#1880
Conversation
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I think a complete fix is only possible in the C core. We need support for attributes with vector values. I proposed this here for 1.0: But realistically, @ntamas and I just don't have the capacity to get this done for the 1.0 release, which is due in September. My suggestion is to not put too much effort into this on the R side until it can be fixed in the C core. Perhaps discourage using @ntamas Are there any hooks in the attribute handler that would allow updating such attributes upon vertex deletion/addition? I don't think there are any. Note that |
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Thanks. I will augment the warning to suggest using x and y and that should be good enough for now |
No, not until we implement some kind of a generic event emitter / listener system that would allow third-party code to hook into anything that happens with a graph. |
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An error would be better here. We discussed before that this should be a vertex attribute, AFAIR this isn't something that the C core currently supports. |
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The R core could support it, though, with #1894. What would it take to make the following code produce the right results? library(igraph, warn.conflicts = FALSE)
g <- make_full_graph(10)
V(g)$layout <- layout_in_circle(g)
plot(g)Created on 2025-06-26 with reprex v2.1.1 |
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Cant remember all discussions here: Should I turn the warning into an error message and then merge? |
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My question in #1880 (comment) is still relevant. |
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I'll investigate but I think this would be a big change.
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1. The code shows it’s possible to store them? 2. We own the plotting code?
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Specifically, this works with #1894: library(igraph, warn.conflicts = FALSE)
g <- make_full_graph(10)
V(g)$layout <- layout_in_circle(g)
V(g)$layout
#> [,1] [,2]
#> [1,] 1.000000 0.000000e+00
#> [2,] 0.809017 5.877853e-01
#> [3,] 0.309017 9.510565e-01
#> [4,] -0.309017 9.510565e-01
#> [5,] -0.809017 5.877853e-01
#> [6,] -1.000000 1.224647e-16
#> [7,] -0.809017 -5.877853e-01
#> [8,] -0.309017 -9.510565e-01
#> [9,] 0.309017 -9.510565e-01
#> [10,] 0.809017 -5.877853e-01Created on 2025-07-05 with reprex v2.1.1 |
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Then let's make it happen. I could adapt the plot code to also check for a vertex layout attribute |
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There are some issue with this approach. Since vector attributes are not supported in C yet, it will not be possible to export these to the standard formats such as GML. In the long term it would be good to do this, but I'm wondering if it's a better approach to wait until the C core supports it, or at least wait until upgrading to C/igraph 1.0. I have an issue open for this here: igraph/igraph#2744 Realistically, we probably won't have the capacity to make it happen for 1.0, but I'd like to be optimistic and take another look ... |
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(To be clear, IMO this is absolutely the right way to do it. My concern is making this an R-specific feature, especially before we had the opportunity to take a good look at it in C and determine what interface is feasible.) |
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We also need to check subsetting and subset assignment for such attributes.
In the other PR.
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We could also make V(g)$layout <- … result in setting the x and y vertex
attributes. Or perhaps create a layout setting function.
I need to review the attribute code to give a better assessment.
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How I envisioned this working was exactly
And of course the biggest issue: Implementing this feature with the very limited capacity we have ... |
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How about going with @krlmlr's design, and setting the |
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Would this be a separate PR? |
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Let's turn this into an error then, and address the other topics later. |
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@krlmlr ok to merge if everything passes? |
krlmlr
changed the title
"layout" attribute doesn't match the number of vertices
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Thanks, merging. |
igraph 2.2.0 Update C core to version 0.10.17. See <https://github.com/igraph/rigraph/blob/20552ef94aed6ae4b23465ae8c7e4d3b0e558c71/src/vendor/cigraph/CHANGELOG.md> for a complete changelog, in particular the section "Breaking changes". - Generate almost all R implementations (#2047). - Expose `align_layout()` and add to `layout_nicely()` to align layout with axis automatically (#1907, #1957, #1958). - Expose `simple_cycles()` which lists all simple cycles (#1573, #1580). - Expose `is_complete()`, `is_clique()` and `is_ivs()` (#1316, #1388, #1581). - Expose `find_cycle()` (#1471, #1571). - Expose `feedback_vertex_set()` to find a minimum feedback vertex set in a graph (#1446, #1447, #1560). - Add `weights` parameter to `local_scan()` (#1082, #1448, #1982). - Add more layouts to `tkplot()` (#160, #1967). - Add `plot(mark.lwd = )` to change line width of mark.groups (#306, #1898). - Add `plot(vertex.label.angle = , vertex.label.adj = )` arguments to rotate vertex labels (#106, #1899). - Add relative size scaling to vertices in `plot()` (@gvegayon, #172). - Split `sample_bipartite()` into two functions for the G(n, m) and G(n, p) case (#630, #1692). - Implement multi attribute assignment (#55, #1916) and adding attributes via data frames (#1373, #1669, #1716). Support factors in `graph_from_data_frame()` (#34, #1829). - All `_hrg()` functions check their argument (#1074, #1699). - HRG printing with `type = "auto"` uses `"plain"` for large trees (#1879). - `get_edge_ids()` accepts data frames and matrices (#1663). - `igraph_version()` returns version of C core in an attribute (#1208, #1781). - Breaking change: change arguments default and order for `graph_from_lcf()` (#1858, #1872). - Breaking change: Subset assignment of a graph avoids addition of double edges and ignores loops unless the new `loops` argument is set to `TRUE` (#1662, #1661). - Breaking change: remove deprecated `neimode` parameter from `bfs()` and `dfs()` (#1105, #1526). - Breaking change: stricter deprecation of non-functional parameters of `layout_with_kk()` and `layout_with_fr()` (#1108, #1628). - `NA` attribute values are replaced with default values in `plot()` (#293, #1707). - `NA` checking only in from/to columns of edge data frame (#1906). - Keep vertex attribute type for `disjoint_union()` (#1640, #1909). - Error in bipartite projection if `type` is not a vertex attribute (#898, #1889). - Do not try to destroy non-initialized SIR objects upon error (#1888). - Added proper `NA` handling for matrix inputs (#917, #918, #1828). - Remove string matrix support from functions operating on biadjacency matrices (#1540, #1542, #1803). - Integer vectors are validated before transferring them to the C library (#1434, #1582). - Changed base location for `graph_from_graphdb()` and added tests (#1712, #1732). - Recycling of logical vectors when indexing into edge/vertex selectors now throws an error (#848, #1731). - Use `function()` instead of `(x)` in `arrow.mode` (#1722). - Temporarily disable generating an interface for `igraph_simple_cycles_callback()` as the framework for handling callback functions is not yet present. - Adjust loop position to vertex size in `plot()` (#1980). - Don't rescale plot coordinates to `[-1,1] x [-1,1]` by default (#1492, #1956, #1962). - Fail if `"layout"` attribute doesn't match the number of vertices (#1880). - Automatically arrange loops in `plot()` (#407, #556, #1881). - Vectorized drawing of arrows in `plot()` (#257, #1904). - Allow more than one edge label font family in `plot()` (#37, #1896). - Pie shapes now work as intended (#1882, #1883). - Loops not plotted on canvas (#1799, #1800). - Replace `NA` values in `label` attributes in `plot()` with default values (#1796, #1797). - Removed duplicated plotting of arrow heads (#640, #1709). - Correct mapping of edge label properties in plots when loops are present (#157, #1706). - Welcome Maëlle Salmon and David Schoch as authors (#1733), add author links (#1821). - Remove demos (#2008). - Add 2023 preprint (#1240, #1984). - Update allcontributors info (#1975). - Link to replacements of deprecated functions (#1823). - Add documentation of all file formats to `read_graph()` and `write_graph()` (#777, #1969). Recommend `saveRDS()` and `readRDS()` for saving and loading graphs (#1242, #1700). - Document return value of `make_clusters()` (#1794). - Clarify that `girth()` returns `Inf` for acyclic graphs (@eqmooring, #1831). - Clarify the use of weights in `layout_with_kk()`. - Refer to current latest version of R in troubleshooting page. - Fix typos in `laplacian_matrix()` documentation. - Document ellipsis in `cohesion()` (#971, #1985). - Correct the description of the `weights` parameter of `hits_scores()`. - Better describe output of `all_shortest_paths()` (#1029, #1778). - `make_graph()` now supports `"Groetzsch"` as an alias of `"Grotzsch"`. This change was implemented in the C core. - Update description of `order` parameter of `ego()` and related functions (#1746). - Added lifecycle table (#1525). - Add more about igraph.r2cdocs in the contributing guide (#1686, #1697). - Accelerate check if an index sequence corresponds to the entire list of vertices (#1427, #1818). - Faster single bracket querying of a graph (#1465, #1658).
Trying to tackle #219.
The overarching issue is that if the layout is saved as a graph attribute (
g$layout), independent on how it is done, there is no checks implemented if the layout matrix can actuallyserve as a layout (that is, if it has the correct number of rows).
This leads to weird behaviour of the plot function.
This PR could be the starting point for a refactoring. Currently, it only adds a warning if the layout does not match the graph. @szhorvat could this be a good start?
Created on 2025-06-24 with reprex v2.1.1