Step 4a - add note about sample names for user friendliness

[mollytest24]

At the chunk to "### Filter the data to samples with at least r params$min_read_count"

filter_low_count_samples <- function(df) {
  # calc read count sums for sample columns
  sample_sums <- df %>% 
    select(starts_with("sample.")) %>%               ###MT here: my sample names begin with "sample_marker.", need to substitute this for "sample."
    summarise(across(everything(), \(x) sum(x, na.rm = TRUE)))
  
  # get names of columns to keep (those with sums >= `min_read_count`)
  columns_to_keep <- sample_sums %>%
    pivot_longer(everything(), names_to = "column", values_to = "sum") %>%
    filter(sum >= params$min_read_count) %>%
    pull(column)
  
  # get all non-sample columns to keep
  non_sample_cols <- names(df)[!grepl("^sample\\.", names(df))].       ###MT here: my sample names being with "sample_marker", need to substitute this for "sample"
  
  # return the filtered df with only samples passing `min_read_count`
  df %>% select(all_of(non_sample_cols), any_of(columns_to_keep))
}

# apply the filtering function
global_keep <- filter_low_count_samples(global_keep)

global_keep$scientific_name <- make.unique(as.character(global_keep$scientific_name))

keep_rows <- nrow(global_keep)
print(paste0("Number of rows kept: ", keep_rows))

We should add a sentence above the chunk or within the lines of code to make this more obvious to new users. Something like:
"# May return an error message if sample names aren't correct. Check global_keep for sample names. Ex. if samples named sample_marker.XYZ001, enter "sample_marker." where code needs sample column header names.

Note that this applies again in the chunk: "## Make a table to represent the counts of each OTU in each sample":

OTU_table <- global_keep[,grep("sample_marker\\.", colnames(global_keep))]    #MT here edit "sample\\." to "sample_marker\\."
names(OTU_table) <- gsub(pattern = "sample_marker.", replacement = "", x = names(OTU_table))    #MT here edit "sample." to "sample_marker."
rownames(OTU_table) <- sub("^", "P", rownames(OTU_table))

And again in "## Make a taxonomy table"

tax_table <- global_keep[,-grep("sample_marker\\.", colnames(global_keep))] #MT changed "sample\\." to "sample_marker\\."
tax_table <- relocate(tax_table, id, definition, {{ best_id_col }}, {{ best_match_col }}, count, .after = last_col())
tax_table2 <- as.matrix(tax_table)
rownames(tax_table2) <- sub("^", "P", rownames(tax_table2))