Plot multiple bivariate relationships in a single plot

This function is designed to accompany rm_uvsum as a means of visualising the results, and uses similar syntax.

plotuv(
  response,
  covs,
  data,
  showN = FALSE,
  showPoints = TRUE,
  na.rm = TRUE,
  response_title = NULL,
  return_plotlist = FALSE,
  ncol = 2,
  p_margins = c(0, 0.2, 1, 0.2),
  bpThreshold = 20,
  mixed = TRUE,
  violin = FALSE,
  position = c("dodge", "stack", "fill"),
  use_labels = TRUE
)

Arguments

response

character vector with names of columns to use for response

covs

character vector with names of columns to use for covariates

data

dataframe containing your data

showN

boolean indicating whether sample sizes should be shown on the plots

showPoints

boolean indicating whether individual data points should be shown when n>20 in a category

na.rm

boolean indicating whether na values should be shown or removed

response_title

character value with title of the plot

return_plotlist

boolean indicating that the list of plots should be returned instead of a plot, useful for applying changes to the plot, see details

ncol

the number of columns of plots to be display in the ggarrange call, defaults to 2

p_margins

sets the TRBL margins of the individual plots, defaults to c(0,0.2,1,.2)

bpThreshold

Default is 20, if there are fewer than 20 observations in a category then dotplots, as opposed to boxplots are shown.

mixed

should a mix of dotplots and boxplots be shown based on sample size? If false then all categories will be shown as either dotplots, or boxplots according the bpThreshold and the smallest category size

violin

Show violin plots instead of boxplots. This will override bpThreshold and mixed.

position

for categorical variables how should barplots be presented. Default is "dodge" IF stack is TRUE then n will not be shown.

use_labels

boolean, default is true if the variables have label attributes this will be shown in the plot instead of the variable names, or if there are no labels then tidy versions of the variable names will be used. If use_labels=FALSE the variable names will be used.

Value

a list containing plots for each variable in covs

Details

Plots are displayed as follows: If response is continuous For a numeric predictor scatterplot For a categorical predictor: If 20+ observations available boxplot, otherwise dotplot with median line If response is a factor For a numeric predictor: If 20+ observations available boxplot, otherwise dotplot with median line For a categorical predictor barplot Response variables are shown on the ordinate (y-axis) and covariates on the abscissa (x-axis)

Variable names are replaced by their labels if available, or by tidy versions if not. Set use_labels=FALSE to use the variable names.

Examples

## Run multiple univariate analyses on the pembrolizumab dataset to predict cbr and
## then visualise the relationships.
data("pembrolizumab")
rm_uvsum(data=pembrolizumab,
response='cbr',covs=c('age','sex','l_size','baseline_ctdna'))
#> <table class="table table" style="margin-left: auto; margin-right: auto; margin-left: auto; margin-right: auto;">
#>  <thead>
#>   <tr>
#>    <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">  </th>
#>    <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> OR(95%CI) </th>
#>    <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> p-value </th>
#>    <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> N </th>
#>    <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Event </th>
#>   </tr>
#>  </thead>
#> <tbody>
#>   <tr>
#>    <td style="text-align:left;"> <span style="font-weight: bold;">Age at study entry</span> </td>
#>    <td style="text-align:right;"> 0.98 (0.94, 1.02) </td>
#>    <td style="text-align:right;"> 0.27 </td>
#>    <td style="text-align:right;"> 94 </td>
#>    <td style="text-align:right;"> 70 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> <span style="font-weight: bold;">Patient Sex</span> </td>
#>    <td style="text-align:right;">  </td>
#>    <td style="text-align:right;">  </td>
#>    <td style="text-align:right;"> 94 </td>
#>    <td style="text-align:right;"> 70 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Female </td>
#>    <td style="text-align:right;"> Reference </td>
#>    <td style="text-align:right;">  </td>
#>    <td style="text-align:right;"> 58 </td>
#>    <td style="text-align:right;"> 46 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Male </td>
#>    <td style="text-align:right;"> 0.52 (0.20, 1.34) </td>
#>    <td style="text-align:right;"> 0.17 </td>
#>    <td style="text-align:right;"> 36 </td>
#>    <td style="text-align:right;"> 24 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> <span style="font-weight: bold;">Target lesion size at baseline</span> </td>
#>    <td style="text-align:right;"> 1.00 (0.99, 1.01) </td>
#>    <td style="text-align:right;"> 0.96 </td>
#>    <td style="text-align:right;"> 94 </td>
#>    <td style="text-align:right;"> 70 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;"> <span style="font-weight: bold;">Baseline ctDNA</span> </td>
#>    <td style="text-align:right;"> 1.00 (1.00, 1.00) </td>
#>    <td style="text-align:right;"> 0.78 </td>
#>    <td style="text-align:right;"> 94 </td>
#>    <td style="text-align:right;"> 70 </td>
#>   </tr>
#> </tbody>
#> </table>
plotuv(data=pembrolizumab,  response='cbr',
covs=c('age','sex','l_size','baseline_ctdna'),showN=TRUE)
#> Warning: Ignoring unknown parameters: `label.size`
#> Warning: Ignoring unknown parameters: `label.size`
#> Warning: Ignoring unknown parameters: `label.size`
#> Warning: `stat(count)` was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(count)` instead.
#> ℹ The deprecated feature was likely used in the reportRmd package.
#>   Please report the issue to the authors.