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Error in mixing_proportions[which(rownames(mixing_proportions) %in% SinkNames), : incorrect number of dimensions #50

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melissaszy opened this issue Mar 9, 2023 · 12 comments
Open

Error in mixing_proportions[which(rownames(mixing_proportions) %in% SinkNames), : incorrect number of dimensions #50

melissaszy opened this issue Mar 9, 2023 · 12 comments

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@melissaszy
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melissaszy commented Mar 9, 2023 •
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Hello,

i downloaded the sample dataset and tried the sample code:
library(FEAST)
setwd("C:/Users/feast_trial")
metadata <- Load_metadata(metadata_path = "metadata_example_multi.txt")
otus <- Load_CountMatrix(CountMatrix_path = "otu_example_multi.txt")
FEAST_output <- FEAST(C = otus, metadata = metadata, different_sources_flag = 1, dir_path = "C:/Users/feast_trial", outfile="demo")
PlotSourceContribution(SinkNames = rownames(FEAST_output)[c(5:8)], SourceNames = colnames(FEAST_output), dir_path = "C:/Users/feast_trial", mixing_proportions = FEAST_output, Plot_title = "Test_",Same_sources_flag = 0, N = 4)

my first issue is when i ran the code above to generate FEAST_output.
the tutorial states that: "FEAST will then save the file demo_FEAST.txt - A file containing an S1 by S2 matrix P, where S1 is the number sinks and S2 is the number of sources (including an unknown source). Each row in matrix P sums to 1."
in my directory, i only have "demo_source_contributions_matrix.txt" file generated.

my second issue is with PlotSourceContribution

i got this error message:
"Error in mixing_proportions[which(rownames(mixing_proportions) %in% SinkNames), :
incorrect number of dimensions"

i am using:
R version 4.2.2
FEAST version 0.1.0

May I ask how what is wrong and how i can fix these issues?

Thank you for your time!
@junzhao23y
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hi! I'm having the same problem as you.
I wonder if you have solved it now?
I'll check and check again in the next few days

@Olivia-hhg
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Olivia-hhg commented Jul 9, 2023 via email

@Olivia-hhg
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Olivia-hhg commented Jul 10, 2023 via email

@Olivia-hhg
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Olivia-hhg commented Jul 10, 2023 via email

@junzhao23y
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junzhao23y commented Jul 17, 2023 via email

@Panda-smile
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同学，我也遇到相同问题，你方便给指导下吗？

@Olivia-hhg
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Olivia-hhg commented Dec 28, 2023 via email

@Panda-smile
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Panda-smile commented Dec 29, 2023 via email

@Olivia-hhg
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Olivia-hhg commented Dec 29, 2023 via email

@Panda-smile
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Panda-smile commented Dec 29, 2023 via email

@NeginValizadegan
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NeginValizadegan commented May 29, 2024 •
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It seems that the demo input files were fixed but the issues persists. Still there is only one output (demo_source_contributions_matrix.txt) and the plot cannot be created because The FEAST_output is a list so doesn't have row and col names. For plot, changing it from rownames(FEAST_output) and colnames(FEAST_output) to rownames(FEAST_output$data_prop) and colnames(FEAST_output$data_prop) will create a plot. Whether this is the plot it was supposed to create, not sure. But even with demo data, we don't get the main output which is proportions of sink in sources.

@abossers-uu
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abossers-uu commented Jun 11, 2024 •
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You can circumvent the plotting problem by LOADING the FEAST output matrix and use that as input for the plot.
See example below:

FEAST_output <- FEAST(C = otus, metadata = metadata, different_sources_flag = 1, dir_path = "./Data_files_out",outfile="demo")
K = 2 #number of sinks to plot
FEAST_output.loaded <- read.table("./Data_files_out/demo_source_contributions_matrix.txt",row.names=1 )
PlotSourceContribution(SinkNames = rownames(FEAST_output.loaded)[c(1:K)],
                       SourceNames = colnames(FEAST_output.loaded), dir_path = "./Data_files_out",
                       mixing_proportions = FEAST_output.loaded, Plot_title = "Test_",Same_sources_flag = 0, N = 2)

To create a bit of sensible plot you can use a boxplot:

out2 <- FEAST_output.loaded %>%
  rownames_to_column("Sink") %>%
  pivot_longer( -Sink, names_to="Source", values_to="Fraction", values_drop_na=TRUE ) %>%
  mutate( "Source" = str_replace_all( Source, "ERR\\d+_", "" ) ) %>%
  mutate( "Sink" = str_replace_all( Sink, "_Env_\\d+$", "" ) ) #%>%

ggplot( out2, aes(Source, Fraction, fill=Source) ) + 
  geom_boxplot( coef=NULL, outlier.colour = NA ) + 
  geom_jitter( width=0.1 ) +
  coord_flip()

Which gives me:
image

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6 participants
@NeginValizadegan @abossers-uu @melissaszy @Olivia-hhg @junzhao23y @Panda-smile