Merge pull request #76 from neilstats/dev

minor updates

.github/workflows/pkgdown.yaml

@@ -22,6 +22,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v1
         with:
           use-public-rspm: true
+          r-version: '4.1.2'
 
       - uses: r-lib/actions/setup-r-dependencies@v1
         with:

DESCRIPTION

@@ -3,7 +3,7 @@ Title: Create CKB Plots
 Description: ckbplotr provides functions to help create and style plots in R.
     It is being developed by, and primarily for, China Kadoorie Biobank 
     researchers.
-Version: 0.6.5
+Version: 0.6.6
 Authors@R: 
     person(given = "Neil",
            family = "Wright",

NEWS.md

@@ -1,4 +1,10 @@
+# ckbplotr 0.6.6
+
+* make_forest_plot() addtext argument can now add multiple tests results and/or text under the same row.
+* README updated.
+
 # ckbplotr 0.6.5
+
 * Added arguments to control the colour of non-data components of a plot.
 * Use R markdown to render plot code to display in Viewer pane of RStudio. (Replacing use of highlight package.)
 * Updates to vignettes.

R/make_forest_plot.R

@@ -68,29 +68,29 @@
 #' @export
 
 make_forest_data <- function(
-  panels,
-  col.key       = "key",
-  row.labels    = NULL,
-  row.labels.levels = c("heading1", "heading2", "heading3"),
-  rows          = NULL,
-  panel.names   = NULL,
-  col.estimate  = "estimate",
-  col.stderr    = "stderr",
-  col.lci       = NULL,
-  col.uci       = NULL,
-  col.left      = NULL,
-  col.right     = NULL,
-  col.keep      = NULL,
-  ci.delim      = ", ",
-  digits        = 2,
-  exponentiate  = TRUE,
-  blankrows     = c(1, 1, 0, 0),
-  scalepoints   = FALSE,
-  minse         = NULL,
-  addtext       = NULL,
-  cols          = panels,
-  headings      = NULL,
-  colnames      = NULL
+    panels,
+    col.key       = "key",
+    row.labels    = NULL,
+    row.labels.levels = c("heading1", "heading2", "heading3"),
+    rows          = NULL,
+    panel.names   = NULL,
+    col.estimate  = "estimate",
+    col.stderr    = "stderr",
+    col.lci       = NULL,
+    col.uci       = NULL,
+    col.left      = NULL,
+    col.right     = NULL,
+    col.keep      = NULL,
+    ci.delim      = ", ",
+    digits        = 2,
+    exponentiate  = TRUE,
+    blankrows     = c(1, 1, 0, 0),
+    scalepoints   = FALSE,
+    minse         = NULL,
+    addtext       = NULL,
+    cols          = panels,
+    headings      = NULL,
+    colnames      = NULL
 ){
 
   # legacy arguments
@@ -120,13 +120,13 @@ make_forest_data <- function(
   if(!is.null(row.labels) & !all(sapply(row.labels[row.labels.levels], is.character))) stop("row.labels.levels columns must be character")
 
   # Make vector of keys after which extra rows are added for addtext
-  extrarowkeys <- c()
   addtextcols <- tibble::tibble(text = character(),
                                 het_dof = character(),
                                 het_stat = character(),
                                 het_p = character(),
                                 trend_stat = character(),
                                 trend_p = character())
+  extrarowkeys <- c()
   if (!is.null(addtext)) {
     for (i in 1:length(addtext)) {
       addtext[[i]] <- dplyr::bind_rows(addtextcols, addtext[[i]]) %>%
@@ -147,12 +147,18 @@ make_forest_data <- function(
         )) %>%
         dplyr::select(key = !!rlang::sym(col.key),
                       .data$addtext) %>%
-        dplyr::mutate(key = as.character(.data$key))
-
-      extrarowkeys <- c(extrarowkeys, addtext[[i]][["key"]])
+        dplyr::mutate(key = as.character(.data$key)) %>%
+        dplyr::group_by(.data$key) %>%
+        dplyr::mutate(addtextrow = 1:dplyr::n() - 1) %>%
+        dplyr::ungroup()
     }
+    extrarowkeys <- purrr::reduce(purrr::map(addtext,
+                                             ~ dplyr::count(., .data$key)),
+                                  dplyr::bind_rows) %>%
+      dplyr::group_by(.data$key) %>%
+      dplyr::summarise(n = max(.data$n))
+    extrarowkeys <- rep(extrarowkeys$key, extrarowkeys$n)
   }
-  extrarowkeys <- unique(extrarowkeys)
 
   # create data frame of row numbers and labels
   if (is.null(row.labels)) {
@@ -247,6 +253,11 @@ make_forest_data <- function(
     }
   }
 
+  out <- out %>%
+    dplyr::group_by(.data$extrarowkey) %>%
+    dplyr::mutate(addtextrow = 1:dplyr::n() - 1) %>%
+    dplyr::ungroup()
+
   # add a blank heading at bottom if needed
   if (utils::tail(out$row.label, 1) != "") {
     out <- out %>%
@@ -255,7 +266,7 @@ make_forest_data <- function(
 
   out <- out %>%
     dplyr::mutate(row = 1:dplyr::n()) %>%
-    dplyr::select(.data$row, .data$row.label, .data$key, .data$extrarowkey)
+    dplyr::select(.data$row, .data$row.label, .data$key, .data$extrarowkey, .data$addtextrow)
 
   # make datatoplot
   datatoplot <- tibble::tibble()
@@ -284,7 +295,10 @@ make_forest_data <- function(
       dplyr::mutate(panel = panel.names[[i]])
 
     if (!is.null(addtext)){
-      out1 <- merge(out1, addtext[[i]], by.x = "extrarowkey", by.y = "key", all.x = TRUE)
+      out1 <- merge(out1, addtext[[i]],
+                    by.x = c("extrarowkey", "addtextrow"),
+                    by.y = c("key", "addtextrow"),
+                    all.x = TRUE)
     } else {
       out1 <- dplyr::mutate(out1, addtext = as.character(NA))
     }
@@ -344,7 +358,7 @@ make_forest_data <- function(
                                 ci.delim,
                                 format(round(uci_transformed, digits), nsmall = digits, trim = T),
                                 ")"))) %>%
-    dplyr::select(-.data$extrarowkey) %>%
+    dplyr::select(-.data$extrarowkey, -.data$addtextrow) %>%
     dplyr::arrange(panel, row)
 
 
@@ -480,80 +494,80 @@ make_forest_data <- function(
 
 
 make_forest_plot <- function(
-  panels,
-  row.labels    = NULL,
-  row.labels.levels = c("heading1", "heading2", "heading3"),
-  rows          = NULL,
-  exponentiate  = TRUE,
-  logscale      = exponentiate,
-  panel.names   = NULL,
-  panel.headings = panel.names,
-  col.key       = "key",
-  col.estimate  = "estimate",
-  col.stderr    = "stderr",
-  col.lci       = NULL,
-  col.uci       = NULL,
-  col.left      = NULL,
-  col.right     = NULL,
-  col.right.parse   = FALSE,
-  col.left.heading  = "",
-  col.right.heading = "HR (95% CI)",
-  col.left.pos    = NULL,
-  col.right.pos   = NULL,
-  col.left.hjust    = 1,
-  col.right.hjust   = 0,
-  col.heading.space = 0,
-  estcolumn     = TRUE,
-  col.keep      = NULL,
-  ci.delim      = ", ",
-  digits        = 2,
-  title         = "",
-  xlab          = "HR (95% CI)",
-  xlim          = NULL,
-  xticks        = NULL,
-  nullval       = NULL,
-  blankrows     = c(1, 1, 0, 0),
-  col.diamond   = NULL,
-  diamond       = NULL,
-  col.bold      = NULL,
-  bold.labels   = NULL,
-  scalepoints   = FALSE,
-  minse         = NULL,
-  pointsize     = 3,
-  shape     = NULL,
-  plotcolour = "black",
-  colour    = NULL,
-  cicolour  = colour,
-  fill      = NULL,
-  ciunder   = NULL,
-  addtext       = NULL,
-  left.space    = NULL,
-  right.space   = NULL,
-  mid.space     = unit(5, "mm"),
-  plot.margin   = margin(8, 8, 8, 8, "mm"),
-  panel.width   = NULL,
-  base_size     = 11,
-  base_line_size = base_size/22,
-  stroke        = 0,
-  printplot     = TRUE,
-  showcode      = TRUE,
-  addcode       = NULL,
-  addaes        = NULL,
-  addarg        = NULL,
-  envir         = NULL,
-  cols          = panels,
-  headings      = NULL,
-  colnames      = NULL,
-  colheadings   = colnames,
-  boldheadings  = NULL,
-  heading.space = NULL,
-  panel.space   = NULL,
-  label.space   = NULL,
-  plot.space    = NULL,
-  col.right.space = NULL,
-  col.left.space  = NULL,
-  margin          = NULL,
-  units          = NULL
+    panels,
+    row.labels    = NULL,
+    row.labels.levels = c("heading1", "heading2", "heading3"),
+    rows          = NULL,
+    exponentiate  = TRUE,
+    logscale      = exponentiate,
+    panel.names   = NULL,
+    panel.headings = panel.names,
+    col.key       = "key",
+    col.estimate  = "estimate",
+    col.stderr    = "stderr",
+    col.lci       = NULL,
+    col.uci       = NULL,
+    col.left      = NULL,
+    col.right     = NULL,
+    col.right.parse   = FALSE,
+    col.left.heading  = "",
+    col.right.heading = "HR (95% CI)",
+    col.left.pos    = NULL,
+    col.right.pos   = NULL,
+    col.left.hjust    = 1,
+    col.right.hjust   = 0,
+    col.heading.space = 0,
+    estcolumn     = TRUE,
+    col.keep      = NULL,
+    ci.delim      = ", ",
+    digits        = 2,
+    title         = "",
+    xlab          = "HR (95% CI)",
+    xlim          = NULL,
+    xticks        = NULL,
+    nullval       = NULL,
+    blankrows     = c(1, 1, 0, 0),
+    col.diamond   = NULL,
+    diamond       = NULL,
+    col.bold      = NULL,
+    bold.labels   = NULL,
+    scalepoints   = FALSE,
+    minse         = NULL,
+    pointsize     = 3,
+    shape     = NULL,
+    plotcolour = "black",
+    colour    = NULL,
+    cicolour  = colour,
+    fill      = NULL,
+    ciunder   = NULL,
+    addtext       = NULL,
+    left.space    = NULL,
+    right.space   = NULL,
+    mid.space     = unit(5, "mm"),
+    plot.margin   = margin(8, 8, 8, 8, "mm"),
+    panel.width   = NULL,
+    base_size     = 11,
+    base_line_size = base_size/22,
+    stroke        = 0,
+    printplot     = TRUE,
+    showcode      = TRUE,
+    addcode       = NULL,
+    addaes        = NULL,
+    addarg        = NULL,
+    envir         = NULL,
+    cols          = panels,
+    headings      = NULL,
+    colnames      = NULL,
+    colheadings   = colnames,
+    boldheadings  = NULL,
+    heading.space = NULL,
+    panel.space   = NULL,
+    label.space   = NULL,
+    plot.space    = NULL,
+    col.right.space = NULL,
+    col.left.space  = NULL,
+    margin          = NULL,
+    units          = NULL
 ){
 
   # legacy arguments

README.Rmd

@@ -99,42 +99,18 @@ install.packages('ckbplotr',
 This will also install dependencies from the CRAN repository.
 
 ### From github
-The latest version of `ckbplotr` can be installed from 
+The latest version of `ckbplotr` can also be installed from 
 github using the `remotes` package.
 ```{r install from github, eval = FALSE}
 install.packages('remotes')
 remotes::install_github('neilstats/ckbplotr')
 ```
 
-If you get an error that reads "Error: Failed to install 'unknown package' from GitHub: HTTP error 404. No commit found for the ref master" then make sure to update to the latest version of the `remotes` package, or try `remotes::install_github('neilstats/ckbplotr@main')`.
-
-If you get an error that reads "Error: (converted from warning) package 'ggplot2' was built under R version ..." you can avoid this by first running `Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true")`. (This is a [known issue](https://github.com/r-lib/remotes/issues/403) with the `remotes` package.) 
-
-### Or from source package
-`ckbplotr` can also be installed from its source package. The R packages  `ggplot2`, `magrittr`, `readr`, `tibble`, `dplyr`, `purrr`,  `rlang`, and `ggtext` must  first be installed.
-```{r install tidyverse, eval = FALSE}
-# The easiest way is to install the whole tidyverse and ggtext:
-install.packages("tidyverse", "ggtext")
-
-# # Or install just these packages:
-# install.packages(c("ggplot2", "readr", "dplyr", "purrr", "ggtext"))
-```
-Then `ckbplotr` can be installed from its source package using the code:
-```{r install from source, eval = FALSE}
-install.packages("ckbplotr.tar.gz", repos = NULL, type = "source")
-```
-Or, in RStudio, open the "Tools" menu and select "Install Packages...".
-In the "Install from..." box select "Package Archive File", and in the
-"Package archive" box browse to the ckbplotr.tar.gz file.
-
-The source package for the latest release version is available [here](https://github.com/neilstats/ckbplotr/releases/latest).
-
-
 ## Get started
 
 Read `vignette("ckbplotr")` to see how to use the `make_shape_plot()`, `make_forest_plot()`, and `plot_like_ckb()` functions.
 
 
 ## ggplot2 code
 
-The `make_shape_plot()` and `make_forest_plot()` functions return both a plot and the ggplot2 code used to create the plot. In RStudio the ggplot2 code used to create the plot will be shown in the Viewer pane (with syntax highlighting if the [highlights](https://cran.r-project.org/package=highlight) package is installed).
+The `make_shape_plot()` and `make_forest_plot()` functions return both a plot and the ggplot2 code used to create the plot. In RStudio the ggplot2 code used to create the plot will be shown in the Viewer pane.