Network plotting function naming

[dimalvovs]

brought from comments in #5

A few additional things I've noticed as I put together vignettes are below. I have been using the PBMC3k data that @jmitchell81 included in the vignette with 25 TFs per cluster and 25 receptors per TF, correlation threshold 0.25 and other parameters default (in case that matters for troubleshooting).

• gene_network plot title is not working for more than one cluster in the clust argument with no OutgoingSignalingClust

gene_network(dom, levels(dom@clusters))

results in the below output:

---

• gene_network plot giving subscript out of bounds error if vectors of clusters are passed to clust and OutgoingSignalingClust. For example:

gene_network(dom, levels(dom@clusters), OutgoingSignalingClust = "CD16_monocyte")

outputs an error:

Error in dom@cl_signaling_matrices[[cl]][, OutgoingSignalingClust] :
subscript out of bounds

---

• signaling_network gives an error requiring finite 'xlim' values when using the showIncomingSignalingClusts argument. For example, if I wanted to look at incoming signal to the CD8 T cell clusters:

signaling_network(dom, showIncomingSignalingClusts = "CD8_T_cell")

OR

signaling_network(dom, clusts = levels(dom@clusters), showIncomingSignalingClusts = "CD8_T_cell")

give an error:

Error in plot.window(...) : need finite 'xlim' values

---

• circos_ligand_receptor is sometimes throwing an error at the step where expression values are obtained from cl_signaling matrices (ex. LILRB2). However, this is inconsistent. For example,

circos_ligand_receptor(dom, receptor = "CD74", cell_colors = cols)

gives output:

but

circos_ligand_receptor(dom, receptor = "LILRB2", cell_colors = cols)

gives error:

Error in data.frame(origin = paste0(cell_names, "-", l), destination = receptor, :
arguments imply differing number of rows: 9, 1, 0

---

I am not sure to what extent these are usage issues on my end (in which case, we should adjust the function documentation to be more precise about what is or isn't allowed, and maybe include more informative error messages as well), but these are all examples of functionality I would expect to work (ie, I wasn't trying to break anything on purpose), so I figure we should look into that. @snag-gh let me know if you need more information or reproducible examples!

Originally posted by @kjkrishnan in #5 (comment)