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m-clark · Aug 17, 2018 · dc3f088 · dc3f088
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diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # visibly 0.2
 
+## visibly 0.2.5
+
+* Add plot_gam_3d.
+
 ## visibly 0.2.4
 
 * Add corr_heat.

diff --git a/R/corr_heat.R b/R/corr_heat.R
@@ -242,7 +242,8 @@ corr_heat <- function(cormat,
       theme_plotly()
 
     # plotly gives a warning it can't do limits, then does them; this appears
-    # the only way to suppress
+    # the only way to suppress, but then won't work for Rmd html output; see
+    # issue #1202
     suppressWarnings({ print(p) })
 
   } else {

diff --git a/README.Rmd b/README.Rmd
@@ -62,23 +62,9 @@ Plot it to get a feel for things.
 create_palette('#ff5500', plot = T)
 ```
 
-There are some other options to express.
-
-```{r plot2}
-create_palette('#ff5500', 
-               alpha = .5, 
-               plot = T, 
-               name = 'orange_you_glad_you_have_this_color')
-```
-
-
 One of the built-in palettes is based on R's blue. Others are based on [Stan's](https://github.com/stan-dev/stan) red, [plotly's](https://github.com/ropensci/plotly) base colors, and the red-blue palette from [RColorBrewer](https://github.com/cran/RColorBrewer/blob/master/R/ColorBrewer.R).
 
 
-```{r rblue}
-palettes$Rblue
-```
-
 A clean theme for <span class="pack">plotly</span>.
 
 ```{r example4}
@@ -89,14 +75,18 @@ mtcars %>%
   theme_plotly()
 ```
 
-Visualize a correlation matrix.
+Visualize a correlation matrix via factor analysis.
 
-```{r corrheat1}
+```{r corrheat1, eval=FALSE}
 data('bfi', package = 'visibly')
 cor_matrix = cor(bfi, use='pair')
 corr_heat(cor_matrix)
 ```
 
+<img src='man/figures/corr_heat.png' style="display:block; margin: 0 auto;" width=50%>
+<br>
+<img src='man/figures/corr_heat_3d.png' style="display:block; margin: 0 auto;" width=50%>
+
 
 Plot some model coefficients.  Requires the <span class="pack">scico</span> package.
 

diff --git a/README.md b/README.md
@@ -101,68 +101,12 @@ create_palette('#ff5500', plot = T)
     $tetradic
     [1] "#FF5500" "#AAFF00" "#00AAFF" "#5500FF"
 
-There are some other options to express.
-
-``` r
-create_palette('#ff5500', 
-               alpha = .5, 
-               plot = T, 
-               name = 'orange_you_glad_you_have_this_color')
-```
-
-<img src="man/figures/README-plot2-1.png" width="75%" style="display: block; margin: auto;" /><img src="man/figures/README-plot2-2.png" width="75%" style="display: block; margin: auto;" />
-
-    $orange_you_glad_you_have_this_color
-    [1] "#FF550080"
-
-    $complementary
-    [1] "#FF550080" "#00AAFF80"
-
-    $analogous
-    [1] "#FF550080" "#FFD50080" "#FF002B80"
-
-    $split_complentary
-    [1] "#FF550080" "#00FFD480" "#002BFF80"
-
-    $triadic
-    [1] "#FF550080" "#00FF5580" "#5500FF80"
-
-    $square
-    [1] "#FF550080" "#2AFF0080" "#00AAFF80" "#D500FF80"
-
-    $tetradic
-    [1] "#FF550080" "#AAFF0080" "#00AAFF80" "#5500FF80"
-
 One of the built-in palettes is based on R’s blue. Others are based on
 [Stan’s](https://github.com/stan-dev/stan) red,
 [plotly’s](https://github.com/ropensci/plotly) base colors, and the
 red-blue palette from
 [RColorBrewer](https://github.com/cran/RColorBrewer/blob/master/R/ColorBrewer.R).
 
-``` r
-palettes$Rblue
-$Rblue
-[1] "#1f65b7"
-
-$complementary
-[1] "#1f65b7" "#b7701f"
-
-$monochromatic
-[1] "#1f65b7" "#366caa" "#4a719e" "#5a7491"
-
-$analogous
-[1] "#1f65b7" "#241fb7" "#1fb2b7"
-
-$split_complementary
-[1] "#1f65b7" "#b2b71f" "#b7241f"
-
-$triadic
-[1] "#1f65b7" "#66b71f" "#b71f66"
-
-$tetradic
-[1] "#1f65b7" "#b7701f" "#66b71f" "#701fb7"
-```
-
 A clean theme for <span class="pack">plotly</span>.
 
 ``` r
@@ -175,15 +119,17 @@ mtcars %>%
 
 <img src="man/figures/README-example4-1.png" width="75%" style="display: block; margin: auto;" />
 
-Visualize a correlation matrix.
+Visualize a correlation matrix via factor analysis.
 
 ``` r
 data('bfi', package = 'visibly')
 cor_matrix = cor(bfi, use='pair')
 corr_heat(cor_matrix)
 ```
 
-<img src="man/figures/README-corrheat1-1.png" width="75%" style="display: block; margin: auto;" />
+<img src='man/figures/corr_heat.png' style="display:block; margin: 0 auto;" width=50%>
+<br>
+<img src='man/figures/corr_heat_3d.png' style="display:block; margin: 0 auto;" width=50%>
 
 Plot some model coefficients. Requires the
 <span class="pack">scico</span> package.

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -16,7 +16,7 @@ highlight: pygments
 
 
 home:
-  strip_header: true
+  #strip_header: true
   links:
   - text: Docs on Stats, R, and more
     href: http://m-clark.github.io
@@ -58,6 +58,7 @@ reference:
       - plot_gam
       - plot_gam_check
       - plot_gam_2d
+      - plot_gam_3d
       - plot_gam_by
 
 figures:

diff --git a/docs/articles/intro.html b/docs/articles/intro.html
diff --git a/docs/articles/intro_files/figure-html/gam-1.png b/docs/articles/intro_files/figure-html/gam-1.png
diff --git a/docs/articles/intro_files/figure-html/gam-2.png b/docs/articles/intro_files/figure-html/gam-2.png
diff --git a/docs/articles/intro_files/figure-html/gam-3.png b/docs/articles/intro_files/figure-html/gam-3.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/corr_heat.html b/docs/reference/corr_heat.html
diff --git a/docs/reference/figures/README-gam-1.png b/docs/reference/figures/README-gam-1.png
diff --git a/docs/reference/figures/README-gam-2.png b/docs/reference/figures/README-gam-2.png
diff --git a/docs/reference/figures/corr_heat.png b/docs/reference/figures/corr_heat.png
diff --git a/docs/reference/figures/corr_heat_3d.png b/docs/reference/figures/corr_heat_3d.png
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/plot_coefficients.brmsfit.html b/docs/reference/plot_coefficients.brmsfit.html
diff --git a/docs/reference/plot_coefficients.html b/docs/reference/plot_coefficients.html
diff --git a/docs/reference/plot_coefficients.lm.html b/docs/reference/plot_coefficients.lm.html
diff --git a/docs/reference/plot_coefficients.merMod.html b/docs/reference/plot_coefficients.merMod.html
diff --git a/docs/reference/plot_gam.html b/docs/reference/plot_gam.html
diff --git a/docs/reference/plot_gam_2d.html b/docs/reference/plot_gam_2d.html