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fix faceting in tm_g_km #720

Merged
merged 15 commits into from
Feb 21, 2023
Merged

fix faceting in tm_g_km #720

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7777c8b
drop wmpty levels before plotting
Feb 15, 2023
3e9d202
Merge branch 'main' into 665_faceting@main
Feb 15, 2023
a8e403d
amend unit tests
Feb 16, 2023
aae213c
minor improvements
Feb 16, 2023
98496af
trigger checks
Feb 16, 2023
057923c
fix
mhallal1 Feb 17, 2023
d59b85d
rewrite plotting
Feb 17, 2023
d16c9e0
improvements
Feb 17, 2023
fcb2eac
option for title construction
Feb 17, 2023
a3a30c3
cleanup
Feb 17, 2023
a40e127
adjust unit tests
Feb 17, 2023
11f2607
add counting function for panel placement
Feb 20, 2023
c4d8b09
change subsetting method for compatibility with older R versions
Feb 20, 2023
a612ab1
styling
Feb 21, 2023
244d899
Merge branch 'main' into 665_faceting@main
mhallal1 Feb 21, 2023
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244 changes: 95 additions & 149 deletions R/tm_g_km.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ template_g_km <- function(dataname = "ANL",
)
)

y$variables <- if (!is.null(strata_var) && length(strata_var) != 0) {
y$variables <- if (length(strata_var) != 0) {
substitute(
expr = variables <- list(tte = tte, is_event = "is_event", arm = arm, strat = strata_var),
env = list(tte = aval_var, arm = arm_var, strata_var = strata_var)
Expand All @@ -108,105 +108,16 @@ template_g_km <- function(dataname = "ANL",
}
graph_list <- list()

if (!is.null(facet_var) && length(facet_var) != 0) {
graph_list <- add_expr(
graph_list,
quote(grid::grid.newpage())
)
graph_list <- add_expr(
graph_list,
substitute(
expr = lyt <- grid::grid.layout(nrow = nlevels(df$facet_var), ncol = 1) %>%
grid::viewport(layout = .) %>%
grid::pushViewport(),
env = list(
df = as.name(dataname),
facet_var = as.name(facet_var)
)
)
)

if (length(facet_var) != 0L) {
graph_list <- add_expr(
graph_list,
substitute(
expr = {
plot_list <- mapply(
df = split(anl, f = anl$facet_var), nrow = seq_along(levels(anl$facet_var)),
FUN = function(df_i, nrow_i) {
if (nrow(df_i) == 0) {
grid::grid.text(
"No data found for a given facet value.",
x = 0.5,
y = 0.5,
vp = grid::viewport(layout.pos.row = nrow_i, layout.pos.col = 1)
)
} else {
g_km(
df = df_i,
variables = variables,
font_size = font_size,
xlab = paste0(
xlab,
" (",
gsub(
"(^|[[:space:]])([[:alpha:]])",
"\\1\\U\\2",
tolower(anl$time_unit_var[1]),
perl = TRUE
),
")"
),
yval = yval,
xticks = xticks,
newpage = FALSE,
title = ifelse(
length(strata_var) == 0,
paste0(title, ", ", quote(facet_var), " = ", as.character(unique(df_i$facet_var))),
paste(
paste0(title, ", ", quote(facet_var), " = ", as.character(unique(df_i$facet_var))),
paste("Stratified by", paste(strata_var, collapse = ", ")),
sep = "\n"
)
),
footnotes = if (annot_coxph) {
paste(
"Ties for Coxph (Hazard Ratio):", ties, "\n",
"p-value Method for Coxph (Hazard Ratio):", pval_method
)
} else {
NULL
},
ggtheme = ggplot2::theme_minimal(),
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
control_surv = control_surv_timepoint(conf_level = conf_level),
control_coxph_pw = control_coxph(conf_level = conf_level, pval_method = pval_method, ties = ties),
ci_ribbon = ci_ribbon,
vp = grid::viewport(layout.pos.row = nrow_i, layout.pos.col = 1),
draw = TRUE
)
}
},
SIMPLIFY = FALSE
)
plot <- tern::stack_grobs(grobs = plot_list)
plot
facets <- droplevels(anl$facet_var)
anl <- split(anl, f = facets)
},
env = list(
font_size = font_size,
facet_var = as.name(facet_var),
strata_var = strata_var,
xticks = xticks,
xlab = xlab,
time_unit_var = as.name(time_unit_var),
yval = yval,
conf_level = conf_level,
pval_method = pval_method,
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
ties = ties,
ci_ribbon = ci_ribbon,
title = title
facet_var = as.name(facet_var)
)
)
)
Expand All @@ -215,67 +126,102 @@ template_g_km <- function(dataname = "ANL",
graph_list,
substitute(
expr = {
plot <- g_km(
df = anl,
variables = variables,
font_size = font_size,
xlab = paste0(
xlab,
" (",
gsub(
"(^|[[:space:]])([[:alpha:]])",
"\\1\\U\\2",
tolower(anl$time_unit_var[1]),
perl = TRUE
facets <- NULL
anl <- list(anl)
}
)
)
}

graph_list <- add_expr(
graph_list,
substitute(
expr = {
grid::grid.newpage()
lyt <- grid::grid.layout(nrow = length(anl), ncol = 1) %>%
grid::viewport(layout = .) %>%
grid::pushViewport()

g_km_counter_generator <- function() {
plot_number <- 0L
function(x) {
plot_number <<- plot_number + 1L
g_km(
x,
variables = variables,
control_surv = control_surv_timepoint(conf_level = conf_level),
xticks = xticks,
xlab = sprintf(
"%s (%s)",
xlab,
gsub("(^|[[:space:]])([[:alpha:]])", "\\1\\U\\2", tolower(x$time_unit_var[1]), perl = TRUE)
),
")"
),
yval = yval,
xticks = xticks,
newpage = TRUE,
ggtheme = ggplot2::theme_minimal(),
control_surv = control_surv_timepoint(conf_level = conf_level),
control_coxph_pw = control_coxph(conf_level = conf_level, pval_method = pval_method, ties = ties),
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
ci_ribbon = ci_ribbon,
title = ifelse(
length(strata_var) == 0,
title,
paste(title, paste("Stratified by", paste(strata_var, collapse = ", ")), sep = "\n")
),
footnotes = if (annot_coxph) {
paste(
"Ties for Coxph (Hazard Ratio):", ties, "\n",
"p-value Method for Coxph (Hazard Ratio):", pval_method
)
} else {
NULL
},
)
plot
},
env = list(
font_size = font_size,
xticks = xticks,
xlab = xlab,
strata_var = strata_var,
time_unit_var = as.name(time_unit_var),
yval = yval,
conf_level = conf_level,
pval_method = pval_method,
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
ties = ties,
ci_ribbon = ci_ribbon,
title = title
yval = yval,
title = sprintf(
"%s%s",
sprintf(
"%s%s",
title,
if (!is.null(facets)) {
sprintf(", %s = %s", as.character(quote(facet_var)), unique(x[[as.character(quote(facet_var))]]))
} else {
""
}
),
if (length(strata_var) != 0) {
sprintf("\nStratified by %s", toString(strata_var))
} else {
""
}
),
footnotes = if (annot_coxph) {
paste(
"Ties for Coxph (Hazard Ratio):", ties, "\n",
"p-value Method for Coxph (Hazard Ratio):", pval_method
)
},
newpage = FALSE,
vp = grid::viewport(layout.pos.row = plot_number, layout.pos.col = 1),
font_size = font_size,
ci_ribbon = ci_ribbon,
ggtheme = ggplot2::theme_minimal(),
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
control_coxph_pw = control_coxph(conf_level = conf_level, pval_method = pval_method, ties = ties)
)
}
}

g_km_counter <- g_km_counter_generator()

plot_list <- lapply(
anl,
g_km_counter
)

plot <- tern::stack_grobs(grobs = plot_list)
plot
},
env = list(
facet_var = if (length(facet_var) != 0L) as.name(facet_var),
font_size = font_size,
strata_var = strata_var,
xticks = xticks,
xlab = xlab,
time_unit_var = as.name(time_unit_var),
yval = yval,
conf_level = conf_level,
pval_method = pval_method,
annot_surv_med = annot_surv_med,
annot_coxph = annot_coxph,
ties = ties,
ci_ribbon = ci_ribbon,
title = title
)
)
}
)

y$graph <- bracket_expr(graph_list)

y
}

Expand Down
107 changes: 54 additions & 53 deletions tests/testthat/test-tm_g_km.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,64 +10,65 @@ testthat::test_that("template_g_km works as expected with default arguments", {
variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARM")
),
graph = quote({
facets <- droplevels(anl$SEX)
anl <- split(anl, f = facets)
grid::grid.newpage()
lyt <- grid::grid.layout(nrow = nlevels(ANL$SEX), ncol = 1) %>%
lyt <- grid::grid.layout(nrow = length(anl), ncol = 1) %>%
grid::viewport(layout = .) %>%
grid::pushViewport()
plot_list <- mapply(
df = split(anl, f = anl$SEX), nrow = seq_along(levels(anl$SEX)),
FUN = function(df_i, nrow_i) {
if (nrow(df_i) == 0) {
grid::grid.text("No data found for a given facet value.",
x = 0.5, y = 0.5, vp = grid::viewport(
layout.pos.row = nrow_i,
layout.pos.col = 1
)
)
} else {
g_km(
df = df_i, variables = variables, font_size = 8,
xlab = paste0(
"Survival time",
" (",
gsub(
"(^|[[:space:]])([[:alpha:]])",
"\\1\\U\\2",
tolower(anl$AVALU[1]),
perl = TRUE
),
")"
), yval = "Survival", xticks = NULL, newpage = FALSE,
title = ifelse(
length(NULL) == 0,
paste0("KM Plot", ", ", quote(SEX), " = ", as.character(unique(df_i$SEX))),
paste(paste0("KM Plot", ", ", quote(SEX), " = ", as.character(unique(df_i$SEX))),
paste("Stratified by", paste(NULL, collapse = ", ")),
sep = "\n"
)
g_km_counter_generator <- function() {
plot_number <- 0L
function(x) {
plot_number <<- plot_number + 1L
g_km(
x,
variables = variables,
control_surv = control_surv_timepoint(conf_level = 0.95),
xticks = NULL,
xlab = sprintf(
"%s (%s)",
"Survival time",
gsub("(^|[[:space:]])([[:alpha:]])", "\\1\\U\\2", tolower(x$AVALU[1]), perl = TRUE)
),
yval = "Survival",
title = sprintf(
"%s%s",
sprintf(
"%s%s",
"KM Plot",
if (!is.null(facets)) {
sprintf(", %s = %s", as.character(quote(SEX)), unique(x[[as.character(quote(SEX))]]))
} else {
""
}
),
footnotes = if (TRUE) {
paste(
"Ties for Coxph (Hazard Ratio):", "efron",
"\n", "p-value Method for Coxph (Hazard Ratio):",
"log-rank"
)
if (length(NULL) != 0) {
sprintf("\nStratified by %s", toString(NULL))
} else {
NULL
},
ggtheme = ggplot2::theme_minimal(), annot_surv_med = TRUE,
annot_coxph = TRUE, control_surv = control_surv_timepoint(conf_level = 0.95),
control_coxph_pw = control_coxph(
conf_level = 0.95,
pval_method = "log-rank", ties = "efron"
),
ci_ribbon = FALSE, vp = grid::viewport(
layout.pos.row = nrow_i,
layout.pos.col = 1
), draw = TRUE
)
}
}, SIMPLIFY = FALSE
""
}
),
footnotes = if (TRUE) {
paste(
"Ties for Coxph (Hazard Ratio):", "efron", "\n",
"p-value Method for Coxph (Hazard Ratio):", "log-rank"
)
},
newpage = FALSE,
vp = grid::viewport(layout.pos.row = plot_number, layout.pos.col = 1),
font_size = 8,
ci_ribbon = FALSE,
ggtheme = ggplot2::theme_minimal(),
annot_surv_med = TRUE,
annot_coxph = TRUE,
control_coxph_pw = control_coxph(conf_level = 0.95, pval_method = "log-rank", ties = "efron")
)
}
}
g_km_counter <- g_km_counter_generator()
plot_list <- lapply(
anl,
g_km_counter
)
plot <- tern::stack_grobs(grobs = plot_list)
plot
Expand Down