Print bone microCT data — print

This is a wrapper around knitr::kable() to print out bone microCT data at one site by sex for use in an R Markdown document. A code chunk containing this function should probably have the results = "asis" option set to allow for pretty formatting.

Usage

print_data(data, ...)

Arguments

data: A 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()).
...: Additional arguments passed on to knitr::kable().

Value

Text output which by default is a Pandoc markdown pipe table for each sex contained in the data supplied. For example:

|   AS|Sex |Genotype | BV/TV|  SMI| Tb.N| Tb.Th| Tb.Sp|
|----:|:---|:--------|-----:|----:|----:|-----:|-----:|
| 1365|M   |Cre      |  5.43| 3.23| 2.46| 0.062| 0.412|
| 1370|M   |Cre      |  6.39| 3.01| 2.59| 0.060| 0.373|
| 1422|M   |Cre      |  8.65| 2.95| 2.81| 0.072| 0.351|
| 1369|M   |Cre;fl   | 12.53| 2.44| 3.33| 0.066| 0.286|
| 1420|M   |Cre;fl   |  6.58| 3.39| 2.68| 0.072| 0.353|
| 1421|M   |Cre;fl   | 14.70| 1.79| 3.23| 0.070| 0.302|




|   AS|Sex |Genotype | BV/TV|  SMI| Tb.N| Tb.Th| Tb.Sp|
|----:|:---|:--------|-----:|----:|----:|-----:|-----:|
| 1366|F   |Cre      |  4.47| 3.73| 2.67| 0.059| 0.371|
| 1372|F   |Cre      |  1.33| 4.40| 1.55| 0.074| 0.666|
| 1373|F   |Cre      |  2.27| 3.36| 2.69| 0.036| 0.373|
| 1367|F   |Cre;fl   |  0.23| 4.17| 1.79| 0.034| 0.558|
| 1368|F   |Cre;fl   |  0.77| 4.08| 2.10| 0.040| 0.482|
| 1371|F   |Cre;fl   |  1.62| 3.43| 1.86| 0.039| 0.527|

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_trab <- read_trabecular_csv(mctr_ex("example-trabecular.csv"),
                                gen_key)
#> Rows: 24 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (19): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (51): 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.
print_data(gen_trab |> dplyr::filter(Site == "Met"))
#> 
#> 
#> |   AS|Sex |Genotype | BV/TV|    SMI|   Tb.N|  Tb.Th|  Tb.Sp|
#> |----:|:---|:--------|-----:|------:|------:|------:|------:|
#> | 1365|M   |Cre      |  5.43| 3.2274| 2.4599| 0.0620| 0.4123|
#> | 1370|M   |Cre      |  6.39| 3.0104| 2.5933| 0.0604| 0.3729|
#> | 1422|M   |Cre      |  8.65| 2.9501| 2.8148| 0.0718| 0.3511|
#> | 1369|M   |Cre;fl   | 12.53| 2.4409| 3.3321| 0.0658| 0.2862|
#> | 1420|M   |Cre;fl   |  6.58| 3.3896| 2.6769| 0.0719| 0.3533|
#> | 1421|M   |Cre;fl   | 14.70| 1.7908| 3.2276| 0.0700| 0.3020|
#> 
#> 
#> 
#> 
#> |   AS|Sex |Genotype | BV/TV|    SMI|   Tb.N|  Tb.Th|  Tb.Sp|
#> |----:|:---|:--------|-----:|------:|------:|------:|------:|
#> | 1366|F   |Cre      |  4.47| 3.7246| 2.6656| 0.0593| 0.3709|
#> | 1372|F   |Cre      |  1.33| 4.4028| 1.5515| 0.0741| 0.6656|
#> | 1373|F   |Cre      |  2.27| 3.3563| 2.6863| 0.0359| 0.3728|
#> | 1367|F   |Cre;fl   |  0.23| 4.1722| 1.7888| 0.0337| 0.5579|
#> | 1368|F   |Cre;fl   |  0.77| 4.0806| 2.0950| 0.0400| 0.4821|
#> | 1371|F   |Cre;fl   |  1.62| 3.4308| 1.8633| 0.0386| 0.5275|
#> 
#>