Open CamilaDuitama opened 2 years ago
hi
the demo data at plot step something wrong
PlotSourceContribution(SinkNames = rownames(FEAST_output)[c(5:8)],SourceNames = colnames(FEAST_output), dir_path = "FEAST-FEAST_beta/Data_files/",mixing_proportions = FEAST_output, Plot_title = "TEST_",Same_sources_flag = 0, N = 4)
Error in mixing_proportions[which(rownames(mixing_proportions) %in% SinkNames), :
I have just tried out with the demo dataset and am getting the same issue in plotting step as @Yixiangzhang1996 . Any updates on this? or suggestions on other code / tutorial datasets to look at to get familiar with using this tool? Thanks ;)
metadata <- Load_metadata(metadata_path = "Data_files/metadata_example_multi.txt") otus <- Load_CountMatrix(CountMatrix_path = "Data_files/otu_example_multi.txt")
FEAST_output <- FEAST(C = otus, metadata = metadata, different_sources_flag = 1, dir_path = "output", outfile="demo_multi")
PlotSourceContribution(SinkNames = rownames(FEAST_output)[c(5:8)], SourceNames = colnames(FEAST_output), dir_path = "output", mixing_proportions = FEAST_output, Plottitle = "Test",Same_sources_flag = 0, N = 4)
plotting step produces this error:
`Error in mixing_proportions[which(rownames(mixing_proportions) %in% SinkNames), :
incorrect number of dimensions`
Hi!
I am interested in getting the overall contribution of each environment source to a sink. For this reason I tried out your demo data with the following R script, by running it 100 times and then parsing the results per sink.
Knowing that FEAST is not a deterministic method, and that there is some expected variability in the results, I wanted to ask you why the results for certain samples vary so much (ex: ERR525698_Env_1). I've attached the results for two of the iterations I calculated (demo90_source_contributions_matrix.txt demo0_source_contributions_matrix.txt).
As you see I always used the same parameters and input data. However, the contribution of Env_2 for the sink mentioned (ERR525698_Env_1) is 0.008 in one iteration and in the other one is 0.798. And this occurs with several other samples.
Is this an expected behaviour?
FEAST version: FEAST_0.1.0
Thank you 👍🏾