Constellation plots full example #78

[salwanbutrus]

Hello,

Thank you so much for making this toolbox publically available! I am trying to make a constellation plot like the ones you have in your papers, but I am having a hard time generating the correct input for the get_knn_graph() function. You provide great example csv files for the plot_constellation() function but none for the knn_graph function. Would you mind providing me with example input to that function so that I can tailor my data accordingly?

Thanks,
Salwan

[yzizhen]

rd.dat is the reduced dimension, with cells in rows, and dimensions as columns. The row names of rd.dat should be the cell_IDs. cl is the cluster assignment, names corresponds to cell_ID, and values are clusters.
result = get_knn_graph(rd.dat, cl=cl, k =50, mc.cores=20)
knn.cl.df = result$knn.cl.df
##prune the KNN graph to clean up constellation
knn.cl.df = knn.cl.df %>% group_by(cl.from) %>% mutate(cl.from.rank = rank(-Freq))
knn.cl.df = knn.cl.df %>% group_by(cl.to) %>% mutate(cl.to.rank = rank(-Freq))
##Keep the edges that have > 0.02 fraction of all in coming edges, or frac > 0.002 and with absolute numbers > 300 that are also among the top 4 incoming or outgoing edges.
select.knn.cl.df = with(knn.cl.df, knn.cl.df[ (frac > 0.02 | frac > 0.002 & Freq > 300) & (cl.from.rank < 4| cl.to.rank < 4),])

[salwanbutrus]

Thanks for your response! I get this error when I try to use the get_knn_graph() function. I can't find the get_knn_batch() function in this repository.

Error in get_knn_batch(rd.dat, ref.rd.dat, k, method = method, batch.size = 10000,  : 
  could not find function "get_knn_batch"

Best,
Salwan

[yzizhen]

It is defined here: https://github.com/AllenInstitute/scrattch.bigcat/blob/master/R/harmonize.R#L84
If you install the scrattch.bigcat package, it should not be a problem.
devtools::install_github("AllenInstitute/scrattch.bigcat")