Plotting actual read counts in Microeco-Class object using original OTU data

[JayalalKJ]

HI, first of all, thank you for developing microeco—it’s a very intuitive and straightforward library, and I have found the scripts easy to work with.

I have a quick question: I would like to plot the original OTU counts (actual read counts) from a microeco-class object instead of relative abundance. Is there a built-in option to do this within the package? If not, could you suggest a method or workaround to achieve this?

[ChiLiubio]

Hi. The cal_abund function can calculate the original abundance to replace relative abundance (rel = FALSE).
Since the calculation of cal_abund is based on the tax_table, we can simply add a column of OTU names to the tax_table.

library(microeco)
data(dataset)
dataset$add_rownames2taxonomy("OTU")
colnames(dataset$tax_table)
# now tax_table in dataset has a new column "OTU"
dataset$cal_abund(rel = FALSE)
View(dataset$taxa_abund$OTU)
# the abundance in this table is same with the original abundance
# taxa_level = "OTU"
t1 <- trans_diff$new(dataset = dataset, method = "anova", group = "Group", taxa_level = "OTU")