Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add option to set reference arm in g_km #1120

Merged
merged 8 commits into from
Nov 2, 2023
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,10 @@
* Added `keep_level_order` split function to retain original order of levels in a split.
* Added `level_order` split function to reorder manually the levels.

### Enhancements
* Added `ref_group_coxph` parameter to `g_km` to specify the reference group used for pairwise Cox-PH calculations when `annot_coxph = TRUE`.
* Added `annot_coxph_ref_lbls` parameter to `g_km` to enable printing the reference group in table labels when `annot_coxph = TRUE`.

### Miscellaneous
* Specified minimal version of package dependencies.

Expand Down
23 changes: 20 additions & 3 deletions R/kaplan_meier_plot.R
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,10 @@
#' * `ties` (`string`)\cr method for tie handling. Default is `"efron"`,
#' can also be set to `"breslow"` or `"exact"`. See more in [survival::coxph()]
#' * `conf_level` (`proportion`)\cr confidence level of the interval for HR.
#' @param ref_group_coxph (`character`)\cr level of arm variable to use as reference group in calculations for
#' `annot_coxph` table. If `NULL` (default), uses the first level of the arm variable.
#' @param annot_coxph_ref_lbls (`flag`)\cr whether the reference group should be explicitly printed in labels for the
#' `annot_coxph` table. If `FALSE` (default), only comparison groups will be printed in `annot_coxph` table labels.
#' @param position_coxph (`numeric`)\cr x and y positions for plotting [survival::coxph()] model.
#' @param position_surv_med (`numeric`)\cr x and y positions for plotting annotation table estimating median survival
#' time per group.
Expand Down Expand Up @@ -204,6 +208,8 @@ g_km <- function(df,
annot_stats = NULL,
annot_stats_vlines = FALSE,
control_coxph_pw = control_coxph(),
ref_group_coxph = NULL,
annot_coxph_ref_lbls = FALSE,
position_coxph = c(-0.03, -0.02),
position_surv_med = c(0.95, 0.9),
width_annots = list(surv_med = grid::unit(0.3, "npc"), coxph = grid::unit(0.4, "npc"))) {
Expand Down Expand Up @@ -383,6 +389,8 @@ g_km <- function(df,
df = df,
variables = variables,
control_coxph_pw = control_coxph_pw,
ref_group_coxph = ref_group_coxph,
annot_coxph_ref_lbls = annot_coxph_ref_lbls,
x = position_coxph[1],
y = position_coxph[2],
width = if (!is.null(width_annots[["coxph"]])) width_annots[["coxph"]] else grid::unit(0.4, "npc"),
Expand Down Expand Up @@ -1348,12 +1356,19 @@ h_grob_y_annot <- function(ylab, yaxis) {
#' @export
h_tbl_coxph_pairwise <- function(df,
variables,
control_coxph_pw = control_coxph()) {
ref_group_coxph = NULL,
control_coxph_pw = control_coxph(),
annot_coxph_ref_lbls = FALSE) {
assert_df_with_variables(df, variables)
checkmate::assert_choice(ref_group_coxph, levels(df[[variables$arm]]), null.ok = TRUE)
checkmate::assert_flag(annot_coxph_ref_lbls)

arm <- variables$arm
df[[arm]] <- factor(df[[arm]])
ref_group <- levels(df[[arm]])[1]
comp_group <- levels(df[[arm]])[-1]

ref_group <- if (!is.null(ref_group_coxph)) ref_group_coxph else levels(df[[variables$arm]])[1]
comp_group <- setdiff(levels(df[[arm]]), ref_group)

results <- Map(function(comp) {
res <- s_coxph_pairwise(
df = df[df[[arm]] == comp, , drop = FALSE],
Expand All @@ -1377,6 +1392,8 @@ h_tbl_coxph_pairwise <- function(df,
row.names(res_df) <- comp
res_df
}, comp_group)
if (annot_coxph_ref_lbls) names(results) <- paste(comp_group, "vs.", ref_group)

do.call(rbind, results)
}

Expand Down
8 changes: 8 additions & 0 deletions man/g_km.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

14 changes: 13 additions & 1 deletion man/h_tbl_coxph_pairwise.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading