intro_refdb.R
In refdb: A DNA Reference Library Manager

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.height = 5,
  fig.width = 7
)

## ----setup, eval=FALSE--------------------------------------------------------
#  library(refdb)
#  library(tidyverse)

## ---- echo=FALSE, message=FALSE-----------------------------------------------
library(refdb)
library(readr)
library(ggplot2)
library(dplyr)
library(forcats)

## ---- include=FALSE-----------------------------------------------------------
lib <- read_csv(system.file("extdata", "ephem.csv", package = "refdb"))

## ---- eval=FALSE--------------------------------------------------------------
#  lib <- read_csv("my_path/ephem.csv")

## -----------------------------------------------------------------------------
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                                     genus = "genus_name",
                                     species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")

## -----------------------------------------------------------------------------
refdb_get_fields(lib)

## -----------------------------------------------------------------------------
lib [91, 1:4]

## -----------------------------------------------------------------------------
lib_na <- refdb_clean_tax_NA(lib)
lib_na [91, 1:4]

## -----------------------------------------------------------------------------
lib [32, 1:4]

## -----------------------------------------------------------------------------
lib_na_extra <- refdb_clean_tax_remove_extra(lib_na)
lib_na_extra [32, 1:4]

## -----------------------------------------------------------------------------
head(lib)

lib_nogap <- refdb_clean_seq_remove_gaps(lib)
head(lib_nogap)

## ---- fig.width=4.5, fig.height=3.5-------------------------------------------
refdb_plot_seqlen_hist(lib)

## -----------------------------------------------------------------------------
lib_long <- refdb_filter_seq_length(lib, min_len = 500)

nrow(lib)
nrow(lib_long)

## -----------------------------------------------------------------------------
refdb_filter_seq_primer(lib, primer_forward = "GGWACWGGWTGAACWGTWTAYCCYCC")

## -----------------------------------------------------------------------------
refdb_filter_seq_primer(lib, primer_forward = "GGWACWGGWTGAACWGTWTAYCCYCC", max_error_forward = 0.2)

## -----------------------------------------------------------------------------
lib %>% 
  group_by(family_name) %>% 
  count() %>% 
  ggplot(aes(fct_reorder(family_name, n, .desc = TRUE), n)) +
  geom_col() +
  xlab("Family") +
  ylab("Number of records") +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))

## ---- message=FALSE, warning=FALSE--------------------------------------------
refdb_plot_tax_treemap(lib)

## ---- message=FALSE, warning=FALSE--------------------------------------------
refdb_plot_tax_tree(lib)

## ---- message=FALSE, warning=FALSE--------------------------------------------
lib <- refdb_set_fields(lib, latitude = "lat", longitude = "lon")
refdb_plot_map(lib)

## ---- eval=FALSE--------------------------------------------------------------
#  refdb_report(lib)

## ---- eval=FALSE--------------------------------------------------------------
#  write_csv(lib, "my_reference_library.csv")

## ---- eval=FALSE--------------------------------------------------------------
#  refdb_write_fields(lib, "my_reference_fields.yml")

## ---- eval=FALSE--------------------------------------------------------------
#  lib <- read_csv("my_reference_library.csv")
#  lib <- refdb_set_fields(lib, config_yaml = "my_reference_fields.yml")