Closed gat2010 closed 2 years ago
Ah I think I know the source of this error, and thank you for posting!
First, can you post the command you tried that caused the error? Include the arguments you used so I can confirm.
I think this error is caused when trying to pass ...
to downstream functions such as jam_igraph()
and ComplexHeatmap::Heatmap()
, except Heatmap()
does not allow ...
so any extra arguments cause an error.
I think your code is something like this:
mem_plot_folio(mem,
node_factor=5,
label_factor=1.5)
There are two workarounds:
node_factor
and label_factor
at this step. You can call the relevant plot function directly and apply customizations, for example with mem_multienrichplot(mem, node_factor=5, label_factor=1.5)
or the same with jam_igraph()
.mem_plot_folio()
with argument do_which
so it does not create the two heatmaps. The heatmaps are created as plot 1 and 2, for example:
mem_plot_folio(mem,
node_factor=5,
label_factor=1.5,
do_which=3:8) # it will create plots 3 through 8
I will update multienrichjam
however I need a fix that will scale well. I probably need to intercept ...
and pass only arguments accepted by ComplexHeatmap::Heatmap()
. Later today or early tomorrow? I want to find a function I can use for that step, I seem to recall a package like dotfiles
or something similar. :)
I feel silly for missing the source of the error, which was the vignette! My mistake, I thought my process using pkgdown::build_site()
would show that, so I must have missed the error.
I made some updates:
call_fn_ellipsis()
...
arguments to Heatmap()
find_colname()
because the vignette was throwing an error.I rebuilt the site docs with pkgdown
to confirm proper handling in the vignette, and function examples.
Update to test:
remotes::install_github("jmw86069/multienrichjam")
And thank you again for posting the issue!
Hi,
I am getting below error while running function mem_canonical_plots
(15:52:37) 23Mar2022: mem_plot_folio(): Enrichment P-value heatmap
(15:52:37) 23Mar2022: mem_plot_folio(): plot_num 1: Enrichment P-value Heatmap
Error in ComplexHeatmap::Heatmap(use_matrix, name = name, col = col_logp, : unused arguments (node_factor = 5, label_factor = 1.5)