siamcat - taxa IDs in check-associations plot
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Last seen 3.0 years ago


thank you for making this very nice tool. I will most likely be using it with my data.

I have a question: I am getting "spXXX" where X are numbers, for genomes /features when checking associations. Is there a way to use the taxa names I have instead? I am simply starting from a dataframe kind of input and it works fine except for the feature labels.

This is how I am importing my counts:

df <- read.csv("~/Desktop/binsclusteringparsingdataframes/dRepagg_bins.csv", na.strings=c("","NA"), check.names = FALSE, stringsAsFactors=FALSE, header = TRUE) rownames(df) <- df[,1] df[,1] <- NULL

then I scale-normalize them, prepare the metadata from the columns of df (my samples names already contain most of the metadata needed). df is what is currently going into siamcat and it seems it is working fine except for the features (taxa) display.

any suggestions?

thank you

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