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7fceb96a83
...
ab189bf59a
16 changed files with 52 additions and 112 deletions
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@ -9,7 +9,7 @@ type: software
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license: AGPL-3.0-or-later
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title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
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with publication ready output'
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version: 25.7.3
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version: 25.7.2
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doi: 10.5281/zenodo.14527429
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identifiers:
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- type: url
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@ -1,6 +1,6 @@
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Package: FreesearchR
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Title: A free and open-source browser based data analysis tool for researchers with publication ready output
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Version: 25.8.1
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Version: 25.7.2
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154")),
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7
NEWS.md
7
NEWS.md
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@ -1,12 +1,7 @@
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# FreesearchR 25.8.2 - DEV
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# FreesearchR 25.7.3 - DEV
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- *NEW* preparing to automatically only show relevant tabs to simplify interface. NOT IMPLEMENTED YET
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# FreesearchR 25.8.1
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- *NEW* improved the use of `wrap_plot_list()` to pass on additional arguments to `patchwork::wrap_plots()` and allowed to specify axes to align in `align_axes()`.
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- *FIX* fixed axis text printed in Euler diagrams
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# FreesearchR 25.7.2
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- *FIX* refining hiding drop downs. All JavaScript is now in separate file. Coded with GAI help from claude.ai.
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@ -1 +1 @@
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app_version <- function()'25.7.3'
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app_version <- function()'25.7.2'
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@ -738,10 +738,7 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
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#' @param data list of ggplot2 objects
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#' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL
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#' @param title panel title
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#' @param guides passed to patchwork::wrap_plots()
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#' @param axes passed to patchwork::wrap_plots()
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#' @param axis_titles passed to patchwork::wrap_plots()
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#' @param ... passed to patchwork::wrap_plots()
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#' @param ... ignored for argument overflow
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#'
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#' @returns list of ggplot2 objects
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#' @export
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@ -750,9 +747,6 @@ wrap_plot_list <- function(data,
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tag_levels = NULL,
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title = NULL,
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axis.font.family = NULL,
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guides = "collect",
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axes = "collect",
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axis_titles = "collect",
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...) {
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if (ggplot2::is_ggplot(data[[1]])) {
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if (length(data) > 1) {
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@ -768,10 +762,9 @@ wrap_plot_list <- function(data,
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})() |>
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align_axes() |>
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patchwork::wrap_plots(
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guides = guides,
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axes = axes,
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axis_titles = axis_titles,
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...
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guides = "collect",
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axes = "collect",
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axis_titles = "collect"
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)
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if (!is.null(tag_levels)) {
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out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
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@ -790,17 +783,13 @@ wrap_plot_list <- function(data,
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cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
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}
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if (!is.null(axis.font.family)) {
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if (inherits(x = out, what = "patchwork")) {
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out <- out &
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ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
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} else {
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out <- out +
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ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
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}
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if (inherits(x = out, what = "patchwork")) {
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out &
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ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
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} else {
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out +
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ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
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}
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out
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}
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@ -811,7 +800,7 @@ wrap_plot_list <- function(data,
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#' @returns list of ggplot2 objects
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#' @export
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#'
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align_axes <- function(..., x.axis = TRUE, y.axis = TRUE) {
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align_axes <- function(...) {
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# https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
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# https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
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if (ggplot2::is_ggplot(..1)) {
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@ -829,16 +818,7 @@ align_axes <- function(..., x.axis = TRUE, y.axis = TRUE) {
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xr <- clean_common_axis(p, "x")
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suppressWarnings({
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purrr::map(p, \(.x){
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out <- .x
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if (isTRUE(x.axis)) {
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out <- out + ggplot2::xlim(xr)
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}
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if (isTRUE(y.axis)) {
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out <- out + ggplot2::ylim(yr)
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}
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out
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})
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p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
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})
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}
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@ -1 +1 @@
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hosted_version <- function()'v25.7.3-250808'
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hosted_version <- function()'v25.7.2-250722'
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@ -76,7 +76,6 @@ ggeulerr <- function(
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#' D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE)
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#' ) |> plot_euler("A", c("B", "C"), "D", seed = 4)
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#' mtcars |> plot_euler("vs", "am", seed = 1)
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#' mtcars |> plot_euler("vs", "am", "cyl", seed = 1)
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plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
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set.seed(seed = seed)
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if (!is.null(ter)) {
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@ -91,9 +90,10 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
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na.omit() |>
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plot_euler_single()
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})
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# browser()
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# names(out)
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wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
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# patchwork::wrap_plots(out)
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# patchwork::wrap_plots(out, guides = "collect")
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}
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#' Easily plot single euler diagrams
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@ -123,8 +123,8 @@ plot_euler_single <- function(data) {
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legend.position = "none",
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# panel.grid.major = element_blank(),
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# panel.grid.minor = element_blank(),
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axis.text.y = ggplot2::element_blank(),
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axis.title.y = ggplot2::element_blank(),
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# axis.text.y = element_blank(),
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# axis.title.y = element_blank(),
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text = ggplot2::element_text(size = 20),
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axis.text = ggplot2::element_blank(),
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# plot.title = element_blank(),
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@ -7,7 +7,6 @@
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#'
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#' @examples
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#' mtcars |> plot_hbars(pri = "carb", sec = "cyl")
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#' mtcars |> plot_hbars(pri = "carb", sec = "cyl", ter="am")
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#' mtcars |> plot_hbars(pri = "carb", sec = NULL)
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plot_hbars <- function(data, pri, sec, ter = NULL) {
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out <- vertical_stacked_bars(data = data, score = pri, group = sec, strata = ter)
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@ -14,19 +14,16 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
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ds <- list(data)
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}
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# browser()
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suppressWarnings({
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out <- lapply(ds, \(.ds){
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rempsyc::nice_violin(
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data = .ds,
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group = sec,
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response = pri,
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xtitle = get_label(data, var = sec),
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ytitle = get_label(data, var = pri)
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)
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})
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wrap_plot_list(out, title = glue::glue("Grouped by {get_label(data,ter)}"))
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out <- lapply(ds, \(.ds){
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rempsyc::nice_violin(
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data = .ds,
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group = sec,
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response = pri,
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xtitle = get_label(data, var = sec),
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ytitle = get_label(data, var = pri)
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)
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})
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wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
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# patchwork::wrap_plots(out,guides = "collect")
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}
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
10
SESSION.md
10
SESSION.md
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@ -15,7 +15,7 @@
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|rstudio |2025.05.0+496 Mariposa Orchid (desktop) |
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|pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
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|quarto |1.7.30 @ /usr/local/bin/quarto |
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|FreesearchR |25.7.3.250722 |
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|FreesearchR |25.7.2.250722 |
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--------------------------------------------------------------------------------
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@ -55,7 +55,6 @@
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|colorspace |2.1-1 |2024-07-26 |CRAN (R 4.4.1) |
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|commonmark |2.0.0 |2025-07-07 |CRAN (R 4.4.1) |
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||||
|crayon |1.5.3 |2024-06-20 |CRAN (R 4.4.1) |
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||||
|credentials |2.0.2 |2024-10-04 |CRAN (R 4.4.1) |
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||||
|curl |6.4.0 |2025-06-22 |CRAN (R 4.4.1) |
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||||
|data.table |1.17.8 |2025-07-10 |CRAN (R 4.4.1) |
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|datamods |1.5.3 |2024-10-02 |CRAN (R 4.4.1) |
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@ -88,19 +87,16 @@
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|foreach |1.5.2 |2022-02-02 |CRAN (R 4.4.0) |
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|foreign |0.8-90 |2025-03-31 |CRAN (R 4.4.1) |
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|Formula |1.2-5 |2023-02-24 |CRAN (R 4.4.1) |
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|FreesearchR |25.7.3 |NA |NA |
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|FreesearchR |25.7.2 |NA |NA |
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|fs |1.6.6 |2025-04-12 |CRAN (R 4.4.1) |
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|gdtools |0.4.2 |2025-03-27 |CRAN (R 4.4.1) |
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||||
|generics |0.1.4 |2025-05-09 |CRAN (R 4.4.1) |
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|gert |2.1.5 |2025-03-25 |CRAN (R 4.4.1) |
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|ggalluvial |0.12.5 |2023-02-22 |CRAN (R 4.4.0) |
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|ggcorrplot |0.1.4.1 |2023-09-05 |CRAN (R 4.4.0) |
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||||
|ggforce |0.5.0 |2025-06-18 |CRAN (R 4.4.1) |
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||||
|ggplot2 |3.5.2 |2025-04-09 |CRAN (R 4.4.1) |
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||||
|ggridges |0.5.6 |2024-01-23 |CRAN (R 4.4.0) |
|
||||
|ggstats |0.10.0 |2025-07-02 |CRAN (R 4.4.1) |
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||||
|gh |1.5.0 |2025-05-26 |CRAN (R 4.4.1) |
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||||
|gitcreds |0.1.2 |2022-09-08 |CRAN (R 4.4.1) |
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|glue |1.8.0 |2024-09-30 |CRAN (R 4.4.1) |
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|gridExtra |2.3 |2017-09-09 |CRAN (R 4.4.1) |
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|gt |1.0.0 |2025-04-05 |CRAN (R 4.4.1) |
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@ -114,7 +110,6 @@
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|htmltools |0.5.8.1 |2024-04-04 |CRAN (R 4.4.1) |
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|htmlwidgets |1.6.4 |2023-12-06 |CRAN (R 4.4.0) |
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|httpuv |1.6.16 |2025-04-16 |CRAN (R 4.4.1) |
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|httr2 |1.2.1 |2025-07-22 |CRAN (R 4.4.1) |
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|IDEAFilter |0.2.0 |2024-04-15 |CRAN (R 4.4.0) |
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|insight |1.3.1 |2025-06-30 |CRAN (R 4.4.1) |
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|iterators |1.0.14 |2022-02-05 |CRAN (R 4.4.1) |
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@ -210,7 +205,6 @@
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|shinyWidgets |0.9.0 |2025-02-21 |CRAN (R 4.4.1) |
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|stringi |1.8.7 |2025-03-27 |CRAN (R 4.4.1) |
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|stringr |1.5.1 |2023-11-14 |CRAN (R 4.4.0) |
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|sys |3.4.3 |2024-10-04 |CRAN (R 4.4.1) |
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|systemfonts |1.2.3 |2025-04-30 |CRAN (R 4.4.1) |
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|testthat |3.2.3 |2025-01-13 |CRAN (R 4.4.1) |
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|textshaping |1.0.1 |2025-05-01 |CRAN (R 4.4.1) |
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@ -49,7 +49,7 @@ library(rlang)
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#### Current file: /Users/au301842/FreesearchR/R//app_version.R
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########
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app_version <- function()'25.7.3'
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app_version <- function()'25.7.2'
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########
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@ -2364,8 +2364,7 @@ wrap_plot_list <- function(data,
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patchwork::wrap_plots(
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guides = "collect",
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axes = "collect",
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axis_titles = "collect",
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...
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axis_titles = "collect"
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)
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if (!is.null(tag_levels)) {
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out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
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|
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@ -2401,7 +2400,7 @@ wrap_plot_list <- function(data,
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#' @returns list of ggplot2 objects
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#' @export
|
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#'
|
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align_axes <- function(...,x.axis=TRUE,y.axis=TRUE) {
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align_axes <- function(...) {
|
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# https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
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# https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
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if (ggplot2::is_ggplot(..1)) {
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@ -2419,16 +2418,7 @@ align_axes <- function(...,x.axis=TRUE,y.axis=TRUE) {
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xr <- clean_common_axis(p, "x")
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suppressWarnings({
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purrr::map(p, \(.x){
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out <- .x
|
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if (isTRUE(x.axis)){
|
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out <- out + ggplot2::xlim(xr)
|
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}
|
||||
if (isTRUE(y.axis)){
|
||||
out <- out + ggplot2::ylim(yr)
|
||||
}
|
||||
out
|
||||
})
|
||||
p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
|
||||
})
|
||||
}
|
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|
||||
|
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@ -4036,7 +4026,7 @@ simple_snake <- function(data){
|
|||
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
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||||
########
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||||
|
||||
hosted_version <- function()'v25.7.3-250808'
|
||||
hosted_version <- function()'v25.7.2-250722'
|
||||
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||||
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||||
########
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||||
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@ -5039,7 +5029,7 @@ plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
|
|||
na.omit() |>
|
||||
plot_euler_single()
|
||||
})
|
||||
# browser()
|
||||
|
||||
# names(out)
|
||||
wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
|
||||
# patchwork::wrap_plots(out, guides = "collect")
|
||||
|
|
@ -5097,7 +5087,6 @@ plot_euler_single <- function(data) {
|
|||
#'
|
||||
#' @examples
|
||||
#' mtcars |> plot_hbars(pri = "carb", sec = "cyl")
|
||||
#' mtcars |> plot_hbars(pri = "carb", sec = "cyl", ter="am")
|
||||
#' mtcars |> plot_hbars(pri = "carb", sec = NULL)
|
||||
plot_hbars <- function(data, pri, sec, ter = NULL) {
|
||||
out <- vertical_stacked_bars(data = data, score = pri, group = sec, strata = ter)
|
||||
|
|
@ -5507,20 +5496,17 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
|
|||
ds <- list(data)
|
||||
}
|
||||
|
||||
# browser()
|
||||
suppressWarnings({
|
||||
out <- lapply(ds, \(.ds){
|
||||
rempsyc::nice_violin(
|
||||
data = .ds,
|
||||
group = sec,
|
||||
response = pri,
|
||||
xtitle = get_label(data, var = sec),
|
||||
ytitle = get_label(data, var = pri)
|
||||
)
|
||||
})
|
||||
|
||||
wrap_plot_list(out, title = glue::glue("Grouped by {get_label(data,ter)}"))
|
||||
out <- lapply(ds, \(.ds){
|
||||
rempsyc::nice_violin(
|
||||
data = .ds,
|
||||
group = sec,
|
||||
response = pri,
|
||||
xtitle = get_label(data, var = sec),
|
||||
ytitle = get_label(data, var = pri)
|
||||
)
|
||||
})
|
||||
|
||||
wrap_plot_list(out,title=glue::glue("Grouped by {get_label(data,ter)}"))
|
||||
# patchwork::wrap_plots(out,guides = "collect")
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
\alias{align_axes}
|
||||
\title{Aligns axes between plots}
|
||||
\usage{
|
||||
align_axes(..., x.axis = TRUE, y.axis = TRUE)
|
||||
align_axes(...)
|
||||
}
|
||||
\arguments{
|
||||
\item{...}{ggplot2 objects or list of ggplot2 objects}
|
||||
|
|
|
|||
|
|
@ -111,7 +111,6 @@ mtcars |> plot_box_single("mpg")
|
|||
mtcars |> plot_box_single("mpg","cyl")
|
||||
gtsummary::trial |> plot_box_single("age","trt")
|
||||
mtcars |> plot_hbars(pri = "carb", sec = "cyl")
|
||||
mtcars |> plot_hbars(pri = "carb", sec = "cyl", ter="am")
|
||||
mtcars |> plot_hbars(pri = "carb", sec = NULL)
|
||||
mtcars |>
|
||||
default_parsing() |>
|
||||
|
|
|
|||
|
|
@ -31,5 +31,4 @@ data.frame(
|
|||
D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE)
|
||||
) |> plot_euler("A", c("B", "C"), "D", seed = 4)
|
||||
mtcars |> plot_euler("vs", "am", seed = 1)
|
||||
mtcars |> plot_euler("vs", "am", "cyl", seed = 1)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -9,9 +9,6 @@ wrap_plot_list(
|
|||
tag_levels = NULL,
|
||||
title = NULL,
|
||||
axis.font.family = NULL,
|
||||
guides = "collect",
|
||||
axes = "collect",
|
||||
axis_titles = "collect",
|
||||
...
|
||||
)
|
||||
}
|
||||
|
|
@ -22,13 +19,7 @@ wrap_plot_list(
|
|||
|
||||
\item{title}{panel title}
|
||||
|
||||
\item{guides}{passed to patchwork::wrap_plots()}
|
||||
|
||||
\item{axes}{passed to patchwork::wrap_plots()}
|
||||
|
||||
\item{axis_titles}{passed to patchwork::wrap_plots()}
|
||||
|
||||
\item{...}{passed to patchwork::wrap_plots()}
|
||||
\item{...}{ignored for argument overflow}
|
||||
}
|
||||
\value{
|
||||
list of ggplot2 objects
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue