version bump

CITATION.cff

@@ -9,7 +9,7 @@ type: software
 license: AGPL-3.0-or-later
 title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers
   with publication ready output'
-version: 25.7.2
+version: 25.7.3
 doi: 10.5281/zenodo.14527429
 identifiers:
 - type: url

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FreesearchR
 Title: A free and open-source browser based data analysis tool for researchers with publication ready output
-Version: 25.7.2
+Version: 25.8.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154")),

NEWS.md

@@ -1,7 +1,12 @@
-# FreesearchR 25.7.3 - DEV
+# FreesearchR 25.8.2 - DEV
 
 - *NEW* preparing to automatically only show relevant tabs to simplify interface. NOT IMPLEMENTED YET
 
+# FreesearchR 25.8.1
+
+- *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()`.
+- *FIX* fixed axis text printed in Euler diagrams
+
 # FreesearchR 25.7.2
 
 - *FIX* refining hiding drop downs. All JavaScript is now in separate file. Coded with GAI help from claude.ai.

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'25.7.2'
+app_version <- function()'25.7.3'

R/data_plots.R

@@ -738,7 +738,10 @@ line_break <- function(data, lineLength = 20, force = FALSE) {
 #' @param data list of ggplot2 objects
 #' @param tag_levels passed to patchwork::plot_annotation if given. Default is NULL
 #' @param title panel title
-#' @param ... ignored for argument overflow
+#' @param guides passed to patchwork::wrap_plots()
+#' @param axes passed to patchwork::wrap_plots()
+#' @param axis_titles passed to patchwork::wrap_plots()
+#' @param ... passed to patchwork::wrap_plots()
 #'
 #' @returns list of ggplot2 objects
 #' @export
@@ -747,6 +750,9 @@ wrap_plot_list <- function(data,
                            tag_levels = NULL,
                            title = NULL,
                            axis.font.family = NULL,
+                           guides = "collect",
+                           axes = "collect",
+                           axis_titles = "collect",
                            ...) {
   if (ggplot2::is_ggplot(data[[1]])) {
     if (length(data) > 1) {
@@ -762,9 +768,10 @@ wrap_plot_list <- function(data,
         })() |>
         align_axes() |>
         patchwork::wrap_plots(
-          guides = "collect",
+          guides = guides,
-          axes = "collect",
+          axes = axes,
-          axis_titles = "collect"
+          axis_titles = axis_titles,
+          ...
         )
       if (!is.null(tag_levels)) {
         out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
@@ -783,13 +790,17 @@ wrap_plot_list <- function(data,
     cli::cli_abort("Can only wrap lists of {.cls ggplot} objects")
   }
 
-  if (inherits(x = out, what = "patchwork")) {
+  if (!is.null(axis.font.family)) {
-    out &
+    if (inherits(x = out, what = "patchwork")) {
-      ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
+      out <- out &
-  } else {
+        ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
-    out +
+    } else {
-      ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
+      out <- out +
+        ggplot2::theme(axis.text = ggplot2::element_text(family = axis.font.family))
+    }
   }
+
+  out
 }
 
 
@@ -800,7 +811,7 @@ wrap_plot_list <- function(data,
 #' @returns list of ggplot2 objects
 #' @export
 #'
-align_axes <- function(...) {
+align_axes <- function(..., x.axis = TRUE, y.axis = TRUE) {
   # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
   # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
   if (ggplot2::is_ggplot(..1)) {
@@ -818,7 +829,16 @@ align_axes <- function(...) {
   xr <- clean_common_axis(p, "x")
 
   suppressWarnings({
-    p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
+    purrr::map(p, \(.x){
+      out <- .x
+      if (isTRUE(x.axis)) {
+        out <- out + ggplot2::xlim(xr)
+      }
+      if (isTRUE(y.axis)) {
+        out <- out + ggplot2::ylim(yr)
+      }
+      out
+    })
   })
 }
 

R/hosted_version.R

@@ -1 +1 @@
-hosted_version <- function()'v25.7.2-250722'
+hosted_version <- function()'v25.7.3-250808'

R/plot_euler.R

@@ -76,6 +76,7 @@ ggeulerr <- function(
 #'   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)
 plot_euler <- function(data, pri, sec, ter = NULL, seed = 2103) {
   set.seed(seed = seed)
   if (!is.null(ter)) {
@@ -90,10 +91,9 @@ 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")
+  # patchwork::wrap_plots(out)
 }
 
 #' Easily plot single euler diagrams
@@ -123,8 +123,8 @@ plot_euler_single <- function(data) {
       legend.position = "none",
       # panel.grid.major = element_blank(),
       # panel.grid.minor = element_blank(),
-      # axis.text.y = element_blank(),
+      axis.text.y = ggplot2::element_blank(),
-      # axis.title.y = element_blank(),
+      axis.title.y = ggplot2::element_blank(),
       text = ggplot2::element_text(size = 20),
       axis.text = ggplot2::element_blank(),
       # plot.title = element_blank(),

R/plot_hbar.R

@@ -7,6 +7,7 @@
 #'
 #' @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)

R/plot_violin.R

@@ -14,16 +14,19 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
     ds <- list(data)
   }
 
-  out <- lapply(ds, \(.ds){
+  # browser()
-    rempsyc::nice_violin(
+  suppressWarnings({
-      data = .ds,
+    out <- lapply(ds, \(.ds){
-      group = sec,
+      rempsyc::nice_violin(
-      response = pri,
+        data = .ds,
-      xtitle = get_label(data, var = sec),
+        group = sec,
-      ytitle = get_label(data, var = pri)
+        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)}"))
+    wrap_plot_list(out, title = glue::glue("Grouped by {get_label(data,ter)}"))
+  })
   # patchwork::wrap_plots(out,guides = "collect")
 }

SESSION.md

@@ -15,7 +15,7 @@
 |rstudio     |2025.05.0+496 Mariposa Orchid (desktop)    |
 |pandoc      |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) |
 |quarto      |1.7.30 @ /usr/local/bin/quarto             |
-|FreesearchR |25.7.2.250722                              |
+|FreesearchR |25.7.3.250722                              |
                                                                                 
                                                                                 
 --------------------------------------------------------------------------------
@@ -55,6 +55,7 @@
 |colorspace        |2.1-1         |2024-07-26 |CRAN (R 4.4.1) |
 |commonmark        |2.0.0         |2025-07-07 |CRAN (R 4.4.1) |
 |crayon            |1.5.3         |2024-06-20 |CRAN (R 4.4.1) |
+|credentials       |2.0.2         |2024-10-04 |CRAN (R 4.4.1) |
 |curl              |6.4.0         |2025-06-22 |CRAN (R 4.4.1) |
 |data.table        |1.17.8        |2025-07-10 |CRAN (R 4.4.1) |
 |datamods          |1.5.3         |2024-10-02 |CRAN (R 4.4.1) |
@@ -87,16 +88,19 @@
 |foreach           |1.5.2         |2022-02-02 |CRAN (R 4.4.0) |
 |foreign           |0.8-90        |2025-03-31 |CRAN (R 4.4.1) |
 |Formula           |1.2-5         |2023-02-24 |CRAN (R 4.4.1) |
-|FreesearchR       |25.7.2        |NA         |NA             |
+|FreesearchR       |25.7.3        |NA         |NA             |
 |fs                |1.6.6         |2025-04-12 |CRAN (R 4.4.1) |
 |gdtools           |0.4.2         |2025-03-27 |CRAN (R 4.4.1) |
 |generics          |0.1.4         |2025-05-09 |CRAN (R 4.4.1) |
+|gert              |2.1.5         |2025-03-25 |CRAN (R 4.4.1) |
 |ggalluvial        |0.12.5        |2023-02-22 |CRAN (R 4.4.0) |
 |ggcorrplot        |0.1.4.1       |2023-09-05 |CRAN (R 4.4.0) |
 |ggforce           |0.5.0         |2025-06-18 |CRAN (R 4.4.1) |
 |ggplot2           |3.5.2         |2025-04-09 |CRAN (R 4.4.1) |
 |ggridges          |0.5.6         |2024-01-23 |CRAN (R 4.4.0) |
 |ggstats           |0.10.0        |2025-07-02 |CRAN (R 4.4.1) |
+|gh                |1.5.0         |2025-05-26 |CRAN (R 4.4.1) |
+|gitcreds          |0.1.2         |2022-09-08 |CRAN (R 4.4.1) |
 |glue              |1.8.0         |2024-09-30 |CRAN (R 4.4.1) |
 |gridExtra         |2.3           |2017-09-09 |CRAN (R 4.4.1) |
 |gt                |1.0.0         |2025-04-05 |CRAN (R 4.4.1) |
@@ -110,6 +114,7 @@
 |htmltools         |0.5.8.1       |2024-04-04 |CRAN (R 4.4.1) |
 |htmlwidgets       |1.6.4         |2023-12-06 |CRAN (R 4.4.0) |
 |httpuv            |1.6.16        |2025-04-16 |CRAN (R 4.4.1) |
+|httr2             |1.2.1         |2025-07-22 |CRAN (R 4.4.1) |
 |IDEAFilter        |0.2.0         |2024-04-15 |CRAN (R 4.4.0) |
 |insight           |1.3.1         |2025-06-30 |CRAN (R 4.4.1) |
 |iterators         |1.0.14        |2022-02-05 |CRAN (R 4.4.1) |
@@ -205,6 +210,7 @@
 |shinyWidgets      |0.9.0         |2025-02-21 |CRAN (R 4.4.1) |
 |stringi           |1.8.7         |2025-03-27 |CRAN (R 4.4.1) |
 |stringr           |1.5.1         |2023-11-14 |CRAN (R 4.4.0) |
+|sys               |3.4.3         |2024-10-04 |CRAN (R 4.4.1) |
 |systemfonts       |1.2.3         |2025-04-30 |CRAN (R 4.4.1) |
 |testthat          |3.2.3         |2025-01-13 |CRAN (R 4.4.1) |
 |textshaping       |1.0.1         |2025-05-01 |CRAN (R 4.4.1) |

inst/apps/FreesearchR/app.R

@@ -49,7 +49,7 @@ library(rlang)
 #### Current file: /Users/au301842/FreesearchR/R//app_version.R 
 ########
 
-app_version <- function()'25.7.2'
+app_version <- function()'25.7.3'
 
 
 ########
@@ -2364,7 +2364,8 @@ wrap_plot_list <- function(data,
         patchwork::wrap_plots(
           guides = "collect",
           axes = "collect",
-          axis_titles = "collect"
+          axis_titles = "collect",
+          ...
         )
       if (!is.null(tag_levels)) {
         out <- out + patchwork::plot_annotation(tag_levels = tag_levels)
@@ -2400,7 +2401,7 @@ wrap_plot_list <- function(data,
 #' @returns list of ggplot2 objects
 #' @export
 #'
-align_axes <- function(...) {
+align_axes <- function(...,x.axis=TRUE,y.axis=TRUE) {
   # https://stackoverflow.com/questions/62818776/get-axis-limits-from-ggplot-object
   # https://github.com/thomasp85/patchwork/blob/main/R/plot_multipage.R#L150
   if (ggplot2::is_ggplot(..1)) {
@@ -2418,7 +2419,16 @@ align_axes <- function(...) {
   xr <- clean_common_axis(p, "x")
 
   suppressWarnings({
-    p |> purrr::map(~ .x + ggplot2::xlim(xr) + ggplot2::ylim(yr))
+      purrr::map(p, \(.x){
+      out <- .x
+      if (isTRUE(x.axis)){
+        out <- out + ggplot2::xlim(xr)
+      }
+      if (isTRUE(y.axis)){
+        out <- out + ggplot2::ylim(yr)
+      }
+      out
+    })
   })
 }
 
@@ -4026,7 +4036,7 @@ simple_snake <- function(data){
 #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R 
 ########
 
-hosted_version <- function()'v25.7.2-250722'
+hosted_version <- function()'v25.7.3-250808'
 
 
 ########
@@ -5029,7 +5039,7 @@ 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")
@@ -5087,6 +5097,7 @@ 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)
@@ -5496,17 +5507,20 @@ plot_violin <- function(data, pri, sec, ter = NULL) {
     ds <- list(data)
   }
 
-  out <- lapply(ds, \(.ds){
+  # browser()
-    rempsyc::nice_violin(
+  suppressWarnings({
-      data = .ds,
+    out <- lapply(ds, \(.ds){
-      group = sec,
+      rempsyc::nice_violin(
-      response = pri,
+        data = .ds,
-      xtitle = get_label(data, var = sec),
+        group = sec,
-      ytitle = get_label(data, var = pri)
+        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)}"))
+    wrap_plot_list(out, title = glue::glue("Grouped by {get_label(data,ter)}"))
+  })
   # patchwork::wrap_plots(out,guides = "collect")
 }
 

man/align_axes.Rd

@@ -4,7 +4,7 @@
 \alias{align_axes}
 \title{Aligns axes between plots}
 \usage{
-align_axes(...)
+align_axes(..., x.axis = TRUE, y.axis = TRUE)
 }
 \arguments{
 \item{...}{ggplot2 objects or list of ggplot2 objects}

man/data-plots.Rd

@@ -111,6 +111,7 @@ 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() |>

man/plot_euler.Rd

@@ -31,4 +31,5 @@ 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)
 }

man/wrap_plot_list.Rd

@@ -9,6 +9,9 @@ wrap_plot_list(
   tag_levels = NULL,
   title = NULL,
   axis.font.family = NULL,
+  guides = "collect",
+  axes = "collect",
+  axis_titles = "collect",
   ...
 )
 }
@@ -19,7 +22,13 @@ wrap_plot_list(
 
 \item{title}{panel title}
 
-\item{...}{ignored for argument overflow}
+\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()}
 }
 \value{
 list of ggplot2 objects