How can I isolate (or filter) a part of a string in several columns at the same time? (in R studio o-CodePudding

I have a data frame with bacteria families from with all their OTUs (phylum, order, family...).

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The data frame is large and I would like the name of each column to be only the last part of each string. The one that starts with "f___"

For example

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I tried some methods in R (like dplyr::filter or filter(str_detect))and also separating columns in Excel and could not get what I wanted. I don't do it manually because it's too many columns.

Thanks

CodePudding user response：

df being your dataframe, you could use rename_with from package dplyr:

df %>%
    rename_with(
        ## your renaming function (see ?gsub for help on
        ## replacing with search patterns (regular expressions):
        ~ gsub('.*;f___(.*)$', '\\1', .x),
        ## column selection (see ?dplyr::select for handy shortcuts)
        cols = everything()
    )

the .x in the replacement formula ~ etc. represents the variable argument to the replacement function, in this case the 'old' column name. You'll encounter this 'dot-something' pattern frequently in tidyverse packages.

CodePudding user response：

microbiota <- read_csv("Tablas/nivel5-familia_clean.csv") colnames(microbiota) <- gsub(colnames(microbiota),pattern = '.*f__', replacement = "")

I solve it like this.