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refactor: stylr and lintr
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@overdodactyl
overdodactyl committed Jan 6, 2024
1 parent 69b1582 commit 191b616
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Showing 29 changed files with 278 additions and 362 deletions.
5 changes: 4 additions & 1 deletion .lintr
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Original file line number Diff line number Diff line change
@@ -1 +1,4 @@
linters: with_defaults(cyclocomp_linter(25))
linters: with_defaults(
line_length_linter(100),
cyclocomp_linter(25)
)
1 change: 0 additions & 1 deletion R/dx_diagnostic_table.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,4 +41,3 @@
#
# return(operatingdata_wide)
# }

92 changes: 31 additions & 61 deletions R/dx_forest.R
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
zero_range <- function (x, tol = 1000 * .Machine$double.eps) {
zero_range <- function(x, tol = 1000 * .Machine$double.eps) {
if (length(x) == 1) {
return(TRUE)
}
if (length(x) != 2)
if (length(x) != 2) {
stop("x must be length 1 or 2")
}
if (any(is.na(x))) {
return(NA)
}
Expand All @@ -17,14 +18,14 @@ zero_range <- function (x, tol = 1000 * .Machine$double.eps) {
if (m == 0) {
return(FALSE)
}
abs((x[1] - x[2])/m) < tol
abs((x[1] - x[2]) / m) < tol
}

rescale <- function (x, to = c(0, 1), from = range(x, na.rm = TRUE, finite = TRUE), ...) {
rescale <- function(x, to = c(0, 1), from = range(x, na.rm = TRUE, finite = TRUE), ...) {
if (zero_range(from) || zero_range(to)) {
return(ifelse(is.na(x), NA, mean(to)))
}
(x - from[1])/diff(from) * diff(to) + to[1]
(x - from[1]) / diff(from) * diff(to) + to[1]
}

#' Create table with odds ratios displayed graphically
Expand Down Expand Up @@ -75,18 +76,17 @@ rescale <- function (x, to = c(0, 1), from = range(x, na.rm = TRUE, finite = TRU
#' dx_plot_forest(dx_obj)
#' dx_plot_forest(dx_obj, trans = "log10")
dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,
tick_label_size = 6.5, trans = c(NA, "log10"),
measures = c("AUC ROC", "Sensitivity", "Specificity","Odds Ratio"),
return = c("ggplot", "grid"),
filename = NA,
header_bg = "white", header_col = "black",
body_bg = c("#e6e4e2", "#ffffff"),
footer_bg = "#b8b6b4", footer_col = "black",
header_fontsize = 10, body_fontsize = 9,
fraction_multiline = FALSE,
or_lwd = .8, or_size = .35,
body_or_col = "black", footer_or_col = footer_col) {

tick_label_size = 6.5, trans = c(NA, "log10"),
measures = c("AUC ROC", "Sensitivity", "Specificity", "Odds Ratio"),
return = c("ggplot", "grid"),
filename = NA,
header_bg = "white", header_col = "black",
body_bg = c("#e6e4e2", "#ffffff"),
footer_bg = "#b8b6b4", footer_col = "black",
header_fontsize = 10, body_fontsize = 9,
fraction_multiline = FALSE,
or_lwd = .8, or_size = .35,
body_or_col = "black", footer_or_col = footer_col) {
check_package("gridExtra")
check_package("grid")
check_package("gtable")
Expand Down Expand Up @@ -152,20 +152,18 @@ dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,
# Format the 'n' column
data$n <- comma(data$n)

# Select and rename the necessary columns. Ensure 'select_measures' is a character vector of column names
cols_to_select <- c("group", "N", select_measuers, " ")
names(data)[names(data) == "n"] <- "N"
tbl_data <- data[cols_to_select]

# Order the columns, moving the space column before 'Odds Ratio'
# Assuming 'Odds Ratio' is one of the 'select_measures'
odds_ratio_index <- which(names(tbl_data) == "Odds Ratio")
space_index <- which(names(tbl_data) == " ")
tbl_data[c("group", "N", select_measuers, " ")]


order <- append(names(tbl_data), " ", after = odds_ratio_index-1)
order <- order[1:length(order)-1]
order <- append(names(tbl_data), " ", after = odds_ratio_index - 1)
order <- order[seq_along(order) - 1]

tbl_data <- tbl_data[order]
rownames(tbl_data) <- NULL
Expand Down Expand Up @@ -210,9 +208,6 @@ dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,
cell_width <- as.data.frame(cell_width)

column_widths <- apply(cell_width, 2, max)
# column_widths[8] <- 0
# column_widths[2] <- column_widths[2] + 5
# column_widths[8] <- max(column_widths)

column_widths <- column_widths / sum(column_widths)

Expand Down Expand Up @@ -308,7 +303,6 @@ dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,
)

if (all(c("Odds Ratio", "Breslow-Day") %in% measures)) {

col <- which(names(tbl_data) == "Odds Ratio")

g <- dx_edit_cell(
Expand All @@ -319,14 +313,12 @@ dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,


# Adjust width of plot - some fine tunining here in the future woud be nice
# g$widths <- grid::unit(rep(1 / ncol(g), ncol(g)), "npc")
g$widths <- grid::unit(column_widths, "npc")
# g$heights <- max(g$heights)

row_height <- ifelse(fraction & fraction_multiline, 1.2, 1)

g$heights <- rep(
grid::unit(0.05*row_height, "npc"),
grid::unit(0.05 * row_height, "npc"),
length(g$heights)
)

Expand All @@ -346,13 +338,9 @@ dx_plot_forest <- function(dx_obj, fraction = FALSE, breaks = NA, limits = NA,

if (return_type == "ggplot") {
g <- dx_forest_to_gg(g)
# print(g)
} else {
# grid::grid.draw(g)
}

return(g)

}


Expand Down Expand Up @@ -417,21 +405,23 @@ dx_edit_cell <- function(table, row, col, name = "core-fg", ...) {

dx_forest_add_or <- function(grob, row, low, est, high,
or_col = 4, col = "black", lwd = .8, pch = 16, size = .35) {

i <- sample(1:100000, 1)

tmp <- dx_hline(
grob, gp = grid::gpar(lwd = lwd, col = col),
grob,
gp = grid::gpar(lwd = lwd, col = col),
y = .5, x0 = low, x1 = high, t = row, l = or_col,
name = paste0("or", i), clip = "on"
)
tmp <- dx_vline(
tmp, gp = grid::gpar(lwd = lwd, col = col),
tmp,
gp = grid::gpar(lwd = lwd, col = col),
x = low, y0 = .35, y1 = .65, t = row, l = or_col,
name = paste0("left_or_cap_", i), clip = "on"
)
tmp <- dx_vline(
tmp, gp = grid::gpar(lwd = lwd, col = col),
tmp,
gp = grid::gpar(lwd = lwd, col = col),
x = high, y0 = .35, y1 = .65, t = row, l = or_col,
name = paste0("right_or_cap_", i), clip = "on"
)
Expand Down Expand Up @@ -474,10 +464,8 @@ dx_forest_add_tick <- function(grob, tick_scaled, tick, nrows,
}

dx_prep_variable <- function(dx_obj, data,
measures = c("AUC-ROC", "Sensitivity", "Specificity","Odds Ratio"),
measures = c("AUC-ROC", "Sensitivity", "Specificity", "Odds Ratio"),
fraction = FALSE, fraction_multiline) {


var <- data$variable[[1]]
orig_var <- data$original_variable[[1]]
tmp <- data[data$measure %in% measures, ]
Expand Down Expand Up @@ -540,31 +528,15 @@ dx_prep_variable <- function(dx_obj, data,
}
}

res[] <- lapply(res, function(x) if(is.factor(x)) as.character(x) else x)

# res$conf_low <- NULL
# res$conf_high <- NULL
# res$n <- NULL
# res$estimate <- NULL
res[] <- lapply(res, function(x) if (is.factor(x)) as.character(x) else x)

res

}

rbind_all <- function(df1, df2) {
df1[setdiff(names(df2), names(df1))] <- NA
df2[setdiff(names(df1), names(df2))] <- NA
rbind(df1, df2)
# # Step 1: Identify all unique column names
# all_cols <- union(names(x), names(y))
#
# # Step 2: Align columns by ensuring both data frames have all columns
# # This fills in any missing columns with NA
# empty_df_aligned <- setNames(lapply(all_cols, function(cn) x[[cn]]), all_cols)
# res_aligned <- setNames(lapply(all_cols, function(cn) y[[cn]]), all_cols)
#
# # Step 3: Bind the rows together
# rbind(empty_df_aligned, res_aligned)
}

label_df <- function(data) {
Expand All @@ -578,7 +550,6 @@ label_df <- function(data) {
}

dx_prep_forest <- function(dx_obj, fraction = fraction, fraction_multiline, measures) {

tmp <- dx_obj$measures[dx_obj$measures$threshold == dx_obj$options$setthreshold, ]


Expand Down Expand Up @@ -682,20 +653,19 @@ plot_labels <- function(breaks, trans) {
}

dx_forest_to_gg <- function(plot, scale = 1, hjust = 0, vjust = 0, ...) {

ymin <- xmin <- 1 - scale
xmax <- ymax <- scale

ggplot2::ggplot(data.frame(x = 0:1, y = 0:1), ggplot2::aes_(x = ~x, y = ~y)) +
ggplot2::geom_blank() +
ggplot2::scale_x_continuous(limits = c(0,1), expand = c(0, 0)) +
ggplot2::scale_y_continuous(limits = c(0,1), expand = c(0, 0)) +
ggplot2::scale_x_continuous(limits = c(0, 1), expand = c(0, 0)) +
ggplot2::scale_y_continuous(limits = c(0, 1), expand = c(0, 0)) +
ggplot2::annotation_custom(
plot,
xmin = xmin + hjust,
xmax = xmax + hjust,
ymin = ymin + vjust,
ymax = ymax + vjust
) +
) +
ggplot2::theme_void()
}
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