Dev

fixing broken links and other rmarkdown rendering issues

…ples

123 triple col is bad for examples

This reverts commit da461df.

…b/dominoSignal into testdata_in_pkgdown_yml

…b/dominoSignal into testdata_in_pkgdown_yml

The revision to the summarize_linkages function had caused each cell to be assigned to its own cluster. This change perserves the original intention of swapping the cell cluster assignments between the first 120 cells with the second set of 120 cells.

…b/dominoSignal into testdata_in_pkgdown_yml

Testdata in pkgdown yml

Report that regulons will not be stored if tf_targets is not a list as a message. This is to avoid an unessesary warning if someone is running dominoSignal without regulons being considered.

silences the warning for cor.test when their are ambiguous ties in the spearman correlation.

The input argument unit tests were throwing warnings because these tiny objects were not present in the data directory. They had been loaded in by the preceeding code, so the tests did not fail. The data call was removed to prevent the spurious warning.

Usage of example() to generate inputs to function helps test that the whole pipeline is working, but the example pages made by roxygen2 are crowded out by reporting every line of code run. Setting echo to false removes all of these extraneous lines.

Minimize domino create warnings

increased edge weights in signaling plot to appear more clearly on examples. Lowered boolean threshold on cor_heatmap to match build parameters.

The verbose option does not silence text from message() output as part of the example code

The inner arcs of the circos plot could not have altered colors because the names of the clusters were being used on the color vector multiple times on line 39. This ambiguity caused a failure to pick a color when more than one color had the cluster name.

dom_clusters(pbmc_dom_built_tiny) returns a character vector, so the levels function had a NULL result.