Package 'chromr'

Check if Column is Present in DataFrame Ignoring Case

Description

Check if Column is Present in DataFrame Ignoring Case

Usage

check_column_exist(data, name)

Arguments

data	Dataframe
name	string of column name

Value

Logical TRUE/FALSE if the column exists.

---

Add Volume Column From Time Units

Description

Adds a column with calculated volums from the time column given a particular flow rate. Currently only constant flow rates are supported.

Usage

chrom_add_volume(.data, flow_rate = 0.5, time = "second")

Arguments

.data	Data frame or tibble with a column called 'time'.
flow_rate	Flow rate in ml/min.
time	Time unit when exported.

Value

a [tibble][tibble::tibble-package]

Examples

fl <- system.file(
  "extdata",
  "sec_no_volume.txt",
  package = "chromr"
)
# read just the data
dat <- fl %>%
  chrom_read_quadtech()
dat
# add a volume given a constant flow rate
dat %>%
  chrom_add_volume(0.3)

---

Append a Chromatogram to Another Run

Description

Sums the volume and the time columns. Optionally continues the numbering of the fractions after the previous runs.

Usage

chrom_append_run(.data, ..., adjust_fractions = FALSE)

Arguments

.data	A data frame created through 'chrom_read_*()'
...	Runs created through 'chrom_read_*()'
adjust_fractions	Logical. FALSE keeps the fraction numbering as-is. TRUE starts the number of the subsequent fractions by adding the previous fractions.

Value

a [tibble][tibble::tibble-package] which combines the given runs.

Examples

fl1 <- system.file("extdata",
  "20220809_SFPQfl_TEVdig_S200_part1.TXT",
  package = "chromr"
)
fl2 <- system.file("extdata",
  "20220809_SFPQfl_TEVdig_S200_part2.TXT",
  package = "chromr"
)
df1 <- chrom_read_quadtech(fl1)
df2 <- chrom_read_quadtech(fl2)


df1 %>%
  chrom_append_run(df2)

---

Find the Line Where Data Begins

Description

Finds the line where the tabular data begins. This is then used to start the reading of the data with 'readr::read_csv()' and end the reading of the metadata.

Usage

chrom_find_data_start_line(file, n_lines = 50)

Arguments

file	File path to the file to read.
n_lines	Number of lines to search for the start of the data.

Value

Single integer of the start of the data.

---

Reads Metadata from QuadTech Chromatogram

Description

Reads Metadata from QuadTech Chromatogram

Usage

chrom_get_meta_quadtech(file, start_line)

Arguments

file	Path to the chromatogram file.
start_line	Start of the data and thus end of the metadata. Determined with 'chromr::chrom_find_data_start_line()'

Value

a [tibble][tibble::tibble-package]

---

Plot a Chromatogram

Description

Plot a Chromatogram

Usage

chrom_plot(data, xlim = NULL, ylim = NULL)

Arguments

data	Data frame that contains columns for wavelength ('wl'), volume ('volume') and absorbance ('abs').
xlim	Limits for the x axis.
ylim	Limits for the y axis.

Value

a 'ggplot2::ggplot()' plot.

Examples

fl <- system.file(
  "extdata",
  "sec_no_volume.txt",
  package = "chromr"
)

fl %>%
  chrom_read_quadtech() %>%
  chrom_add_volume(0.3) %>%
  chrom_plot(xlim = c(0, 3), ylim = c(NA, 0.01))

---

Plot Chromatogram with Fractions

Description

Plot Chromatogram with Fractions

Usage

chrom_plot_fractions(
  data,
  wl_frac = 280,
  fractions = TRUE,
  frac_include = "all",
  frac_labelling = 5,
  frac_text_size = 3,
  frac_text_adjust = 1.3
)

Arguments

data	Datafram containing values.
wl_frac	Wavelengths to show the fractionation scheme for.
fractions	Logical, whether to incude fractions on the plot.
frac_include	Specific fractions to include. Either "all" for all fractions, or a numeric vector of length 2, specifying the limits for the fractions to be included (e.g. c(10, 30) includes fractions from 10 till 30, including both).
frac_labelling	How often to label the fractions. Every $n_th$ fraction is labelled.
frac_text_size	Size of the labels for the fractionation.
frac_text_adjust	'vjust' for the labels for the fractionation.

Value

a ggplot object.

Examples

fl1 <- system.file("extdata",
  "20220809_SFPQfl_TEVdig_S200_part1.TXT",
  package = "chromr"
)
fl2 <- system.file("extdata",
  "20220809_SFPQfl_TEVdig_S200_part2.TXT",
  package = "chromr"
)
df1 <- chrom_read_quadtech(fl1)
df2 <- chrom_read_quadtech(fl2)
dat <- chrom_append_run(df1, df2)
chrom_plot_fractions(dat, wl_frac = c(280, 488))

---

Read .csv Chromatogram from the BioRad NGC

Description

Read .csv Chromatogram from the BioRad NGC

Usage

chrom_read_ngc(file, skip = 1)

Arguments

file	File path to the '.csv' file.
skip	Number of lines to skip before begin reading. Usually 1 line.

Value

a [tibble][tibble::tibble-package]

Examples

fl <- system.file(
  "extdata",
  "ngc_sec.csv",
  package = "chromr"
)

dat <- chrom_read_ngc(fl)
dat

---

Read BioRad QuadTech Chromatogram Files

Description

Read BioRad QuadTech Chromatogram Files

Usage

chrom_read_quadtech(file, interp_volume = TRUE)

Arguments

file	Exported '.TXT' chromatogram file from the BioRad QuadTech.
interp_volume	Logical. If TRUE, interpolates the values in the volume column based on the values in the time column.

Value

a [tibble][tibble::tibble-package]

Examples

fl <- system.file("extdata",
  "sec.txt",
  package = "chromr"
)
# just read
fl %>%
  chrom_read_quadtech()

# read without interpolating volume
fl %>%
  chrom_read_quadtech(interp_volume = FALSE)
# read then plot
fl %>%
  chrom_read_quadtech() %>%
  chrom_plot()

---

Interpolate Interpolate Given Column

Description

Interpolate Interpolate Given Column

Usage

interpolate_column(data, col)

Arguments

data	Dataframe with column to interpolate.
col	Name of the column to interpolate.

Value

a [tibble][tibble::tibble-package]

---

Title

Description

Title

Usage

rename_columns(data)

Arguments

data	Dataframe to rename the columns of.

Value

Dataframe with renamed column.

---