Point-range plots with type="pr" (#35)

* pointrange

* news

* Skip density plot tests in R dev (#36)

- To help with failing CI tests on development run.
- See https://bugs.r-project.org/show_bug.cgi?id=18337

* PR review

* readme update

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: plot2
 Type: Package
 Title: Lightweight extension of base R plot
-Version: 0.0.2.9006
+Version: 0.0.2.9007
 Authors@R: 
   c(
     person(

NEWS.md

@@ -16,6 +16,7 @@ New features:
 - Both the `pch` and `lty` arguments now accept a "by" convenience keyword for
 automatically adjusting plot characters and line types by groups (#28,
 @grantmcdermott).
+- Point-range plots with `type="pointrange"` (#35 @vincentarelbundock)
 
 Bug fixes:
 

R/by_aesthetics.R

@@ -71,7 +71,7 @@ by_col = function(ngrps = 1L, col = NULL, palette = NULL) {
 by_pch = function(ngrps, type, pch=NULL) {
 
   no_pch = FALSE
-  if (!type %in% c("p", "b", "o")) {
+  if (!type %in% c("p", "b", "o", "pointrange")) {
     no_pch = TRUE
     pch = NULL
 

R/plot2.R

@@ -26,8 +26,8 @@
 #'   following values are possible, for details, see plot: "p" for points, "l"
 #'   for lines, "b" for both points and lines, "c" for empty points joined by
 #'   lines, "o" for overplotted points and lines, "s" and "S" for stair steps
-#'   and "h" for histogram-like vertical lines. Finally, "n" does not produce
-#'   any points or lines.
+#'   and "h" for histogram-like vertical lines. "n" does not produce
+#'   any points or lines. "pointrange" draws point-range plots.
 #' @param xlim the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed
 #'   and leads to a ‘reversed axis’. The default value, NULL, indicates that
 #'   the range of the `finite` values to be plotted should be used.
@@ -94,6 +94,7 @@
 #'   be calling `dev.off()` to reset all `par` settings to their defaults.)
 #' @param subset,na.action,drop.unused.levels arguments passed to `model.frame`
 #'   when extracting the data from `formula` and `data`.
+#' @param ymin,ymax minimum and maximum coordinates of the point range. Only used when `type="pointrange"`.
 #' @param ... 	other `graphical` parameters (see `par` and also the "Details"
 #'   section of `plot`).
 #'   
@@ -241,6 +242,8 @@ plot2.default = function(
     col = NULL,
     lty = NULL,
     par_restore = FALSE,
+    ymin = NULL,
+    ymax = NULL,
     ...) {
 
   if (is.null(y)) {
@@ -255,12 +258,18 @@ plot2.default = function(
 
   if (is.null(xlim)) xlim = range(x, na.rm = TRUE)
   if (is.null(ylim)) ylim = range(y, na.rm = TRUE)
-
+
+  if (!is.null(ymin)) ylim[1] = min(c(ylim, ymin))
+  if (!is.null(ymax)) ylim[2] = max(c(ylim, ymax))
+
   if (!is.null(by)) {
-    split_data = lapply(list(x=x, y=y), split, by)
+    l = list(x=x, y=y)
+    l[["ymin"]] = ymin
+    l[["ymax"]] = ymax
+    split_data = lapply(l, split, by)
     split_data = do.call(function(...) Map("list", ...), split_data)
   } else {
-    split_data = list(list(x=x, y=y))
+    split_data = list(list(x=x, y=y, ymin = ymin, ymax = ymax))
   }
 
   ngrps = length(split_data)
@@ -399,7 +408,22 @@ plot2.default = function(
   if (!is.null(grid)) grid
 
   # draw the points/lines
-  if (type == "p") {
+  if (type %in% "pointrange") { # segments before point
+    invisible(
+      lapply(
+        seq_along(split_data),
+        function(i) {
+          graphics::segments(
+            x0 = seq_along(split_data[[i]]$x),
+            y0 = split_data[[i]]$ymin,
+            x1 = seq_along(split_data[[i]]$x),
+            y1 = split_data[[i]]$ymax
+          )
+        }
+      )
+    )
+  } 
+  if (type %in% c("p", "pointrange")) {
     invisible(
       lapply(
         seq_along(split_data),
@@ -415,8 +439,7 @@ plot2.default = function(
         }
       )
     )
-  }
-  if (type %in% c("l", "o", "b", "c", "h", "s", "S")) {
+  } else if (type %in% c("l", "o", "b", "c", "h", "s", "S")) {
     invisible(
       lapply(
         seq_along(split_data),
@@ -432,6 +455,8 @@ plot2.default = function(
         }
       )
     )
+  } else {
+    stop("`type` argument not supported.", call. = FALSE)
   }
 
   title(

README.Rmd

@@ -79,6 +79,8 @@ Let's load the package then walk through some examples.
 library(plot2)
 ```
 
+### Similarity to `plot()`
+
 As far as possible, `plot2` tries to be a drop-in replacement for regular `plot`
 calls.
 
@@ -103,6 +105,8 @@ plot2(Temp ~ Day, data = airquality, main = "plot2 (formula)")
 dev.off() # reset to default (single) plot window
 ```
 
+### Grouped data
+
 So far, so good. But where `plot2` starts to diverge from its base counterpart is
 with respect to grouped data. In particular, `plot2` allows you to characterize
 groups using the `by` argument.^[At this point, experienced base plot users 
@@ -168,6 +172,8 @@ plot2(
 )
 ```
 
+### Colors
+
 On the subject of group colours, these are easily customized via the `palette`
 argument. The default group colours are inherited from either the "R4" or
 "Viridis" palettes, depending on the number of groups. However, all of the many
@@ -190,6 +196,8 @@ Beyond these convenience strings, users can also supply a valid
 palette-generating function for finer control over transparency, colour order,
 and so forth. We'll see a demonstration of this further below.
 
+### Legend
+
 In all of the preceding plots, you will have noticed that we get an automatic
 legend. The legend position and look can be customized using appropriate
 arguments. You can change (or turn off) the legend title and bounding box,
@@ -219,6 +227,27 @@ with(airquality, plot2(
 ))
 ```
 
+### Point-range
+
+`plot2` adds a new `type="pointrange"` option to draw point-ranges plots:
+
+```{r pointrange, warning = FALSE}
+mod = lm(mpg ~ hp + factor(cyl), mtcars)
+coefs = data.frame(names(coef(mod)), coef(mod), confint(mod))
+coefs = setNames(coefs, c("x", "y", "ymin", "ymax"))
+with(coefs,
+  plot2(pch = 17,
+        x = 1:4,
+        y = y,
+        ymin = ymin,
+        ymax = ymax,
+        type = "pointrange"
+  )
+)
+```
+
+### Customization
+
 Customizing your plots further is straightforward, whether that is done by
 changing global parameters or invoking `plot2` arguments. Here's a quick
 penultimate example, where we change our point character and font family
@@ -266,6 +295,8 @@ basetheme(NULL)  # back to default theme
 dev.off()
 ```
 
+## Conclusion
+
 In summary, consider the **plot2** package if you are looking for base R `plot`
 functionality with some added convenience features. You can use pretty much the
 same syntax and all of your theming elements should carry over too. It has no

README.md

@@ -72,6 +72,8 @@ Let’s load the package then walk through some examples.
 library(plot2)
 ```
 
+### Similarity to `plot()`
+
 As far as possible, `plot2` tries to be a drop-in replacement for
 regular `plot` calls.
 
@@ -105,6 +107,8 @@ dev.off() # reset to default (single) plot window
 #>           1
 ```
 
+### Grouped data
+
 So far, so good. But where `plot2` starts to diverge from its base
 counterpart is with respect to grouped data. In particular, `plot2`
 allows you to characterize groups using the `by` argument.[^1]
@@ -170,6 +174,8 @@ plot2(
 
 <img src="man/figures/README-by_lty-1.png" width="100%" />
 
+### Colors
+
 On the subject of group colours, these are easily customized via the
 `palette` argument. The default group colours are inherited from either
 the “R4” or “Viridis” palettes, depending on the number of groups.
@@ -191,6 +197,8 @@ Beyond these convenience strings, users can also supply a valid
 palette-generating function for finer control over transparency, colour
 order, and so forth. We’ll see a demonstration of this further below.
 
+### Legend
+
 In all of the preceding plots, you will have noticed that we get an
 automatic legend. The legend position and look can be customized using
 appropriate arguments. You can change (or turn off) the legend title and
@@ -226,6 +234,30 @@ with(airquality, plot2(
 
 <img src="man/figures/README-desnity_topright-1.png" width="100%" />
 
+### Point-range
+
+`plot2` adds a new `type="pointrange"` option to draw point-ranges
+plots:
+
+``` r
+mod = lm(mpg ~ hp + factor(cyl), mtcars)
+coefs = data.frame(names(coef(mod)), coef(mod), confint(mod))
+coefs = setNames(coefs, c("x", "y", "ymin", "ymax"))
+with(coefs,
+  plot2(pch = 17,
+        x = 1:4,
+        y = y,
+        ymin = ymin,
+        ymax = ymax,
+        type = "pointrange"
+  )
+)
+```
+
+<img src="man/figures/README-pointrange-1.png" width="100%" />
+
+### Customization
+
 Customizing your plots further is straightforward, whether that is done
 by changing global parameters or invoking `plot2` arguments. Here’s a
 quick penultimate example, where we change our point character and font
@@ -283,6 +315,8 @@ dev.off()
 #>           1
 ```
 
+## Conclusion
+
 In summary, consider the **plot2** package if you are looking for base R
 `plot` functionality with some added convenience features. You can use
 pretty much the same syntax and all of your theming elements should

inst/tinytest/test-pointrange.R

@@ -0,0 +1,19 @@
+source("helpers.R")
+using("tinysnapshot")
+
+mod = lm(mpg ~ hp + factor(cyl), mtcars)
+coefs = data.frame(names(coef(mod)), coef(mod), confint(mod))
+coefs = setNames(coefs, c("x", "y", "ymin", "ymax"))
+
+fun = function() {
+    with(
+        coefs,
+        plot2(
+            pch = 17,
+            x = 1:4,
+            y = y,
+            ymin = ymin,
+            ymax = ymax,
+            type = "pointrange"))
+}
+expect_snapshot_plot(fun, label = "pointrange_triangle")