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Plot bone microCT data by genotype or treatment

plot_groups.Rd

This function takes in bone microCT data and produces boxplots comparing two genotypes or treatments.

Usage

plot_groups(data, type = NULL, title = "sex", x_axis_angle = 45)

Arguments

data

A tibble/data frame containing bone microCT data, formatted as is the output of read_trabecular_csv(), read_cortical_csv(), or read_mfe_csv() (or read_*_excel()).

type

A string indicating the type of data supplied. Options include trabecular, cortical, or fea. Alternatively, a specific microCT measure of interest can be specified (e.g., Ct.vBMD). Defaults to NULL, in which case the function will try to figure out which type of data it is.

title

A string indicating what type of title the plots should have. Defaults to sex, which is currently the only option implemented. To remove titles from the plots, set title to NULL.

x_axis_angle

The angle at which to rotate the x-axis labels so they don't overlap, passed on to ggplot2::theme() as axis.text.x = element_text(angle = x_axis_angle).

Value

A list containing ggplot2::ggplot() objects for sex each analyzed. To print each plot without printing the list index, see print_plots().

Details

If the two genotypes or treatments are significantly different, statistical significance will be indicated with "*" if P < 0.05, "**" if P < 0.01, or "***" if P < 0.001.

Examples

gen_key <- read_key_csv(mctr_ex("example-gen-key.csv"))
#> Rows: 12 Columns: 7
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (2): Sex, Genotype
#> dbl (5): AS, SampNo, Spine, Met, Dia
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
gen_cort <- read_cortical_csv(mctr_ex("example-twice1.csv"),
                          mctr_ex("example-twice2.csv"),
                          gen_key)
#> Rows: 36 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (44): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (26): SampNo, MeasNo, Integr.Time, Sigma, Support, Threshold, Unit, Data...
#> lgl  (5): S-DOB, S-Remark, Meas-Rmk, RAW-Label, IMA-Label
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 36 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (43): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (27): SampNo, MeasNo, Integr.Time, Sigma, Support, Threshold, Unit, Data...
#> lgl  (5): S-DOB, S-Remark, Meas-Rmk, RAW-Label, IMA-Label
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
plot_groups(gen_cort |> dplyr::filter(Site == "Dia"))
#> $M

#> 
#> $F

#>