Merge pull request #77 from selkamand/joss

Joss

paper/PaperFigures.qmd

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+---
+title: "PaperFigures"
+format: html
+editor: visual
+---
+
+## Figures for Paper
+
+```{r}
+library(gg1d)
+library(here)
+```
+
+## Figure 1
+
+```{r, fig.height=5, fig.width=10}
+figure1a <- gg1d(
+  iris, show_legend = TRUE, 
+    fontsize_y_text = 24,
+    fontsize_barplot_y_numbers = 0, 
+    legend_text_size = 24,  
+    legend_position = "bottom",
+    legend_key_size = 1.2, 
+    relative_height_numeric = 2,
+    legend_nrow = 1,
+    na_marker_size = 14,
+  interactive_svg_height = 5, interactive_svg_width = 10,
+  )
+
+figure1a
+
+# ggsaves::ggisaves(figure1a, prefix = "figure1a", outfolder = here("paper/"), dpi = 300, title = "Iris")
+```
+
+```{r, fig.height=5, fig.width=8}
+library(datarium)
+
+# Change Columns Order to choose which features appear first
+titanic.raw <- titanic.raw[c("Survived", "Sex", "Age", "Class")]
+
+# Resort columns in the way (replace with multipl args to col_sort at one point
+titanic.raw <- titanic.raw |>
+  dplyr::arrange(Survived, Sex, Age, Class)
+
+figure1b <- gg1d(
+  titanic.raw,
+  palettes = list(
+    Sex = c(Male = "#0072B2", Female = "#CC79A7"),
+    Survived = c(Yes = "#32A02D", No ="#E31A1C"),
+    # Class = c("Crew" =  "#F9F7EAFF", "1st" ="#006E37FF", "2nd" = "#8DB580FF", "3rd" =  "#D9E5BDFF"),
+    # Class = c("Crew" =  "#F9F7EAFF", "1st" = "#005A2FFF", "2nd" = "#719A63FF", "3rd" = "#C0D6A8FF"),
+  Class = c("Crew" =  "#F9F7EAFF", "1st" = "#004826FF", "2nd" = "#5D7C50FF", "3rd" = "#A8BE93FF"),
+    Age = c(Child = "#35B779FF",  Adult = "#440154FF")
+    ), 
+
+  show_legend = TRUE,
+  fontsize_y_text = 24,
+  fontsize_barplot_y_numbers = 0, 
+  legend_nrow = 2,
+  legend_text_size = 24,
+  interactive_svg_height = 5, interactive_svg_width = 8
+  )
+
+figure1b
+
+ggsaves::ggisaves(figure1b, prefix = "figure1b", outfolder = here("paper/"), dpi = 300, title = "Titanic")
+```
+
+```{r, fig.height = 4, fig.width = 16}
+# Drop Year Column
+library(palmerpenguins)
+penguins$year <- NULL
+
+# Subsample
+# penguins2 <- penguins[sample(seq_len(nrow(penguins)), size = 200),]
+  
+figure1c <- gg1d(
+  penguins, 
+  show_legend = TRUE, 
+  fontsize_y_text = 24,
+  fontsize_barplot_y_numbers = 0, 
+  legend_text_size = 24,  
+  legend_key_size = 1.2, 
+  relative_height_numeric = 1,col_sort = "species",
+  legend_nrow = 1,
+  na_marker_size = 14,
+  interactive_svg_height = 4, 
+  interactive_svg_width = 16,
+  na_marker_colour = "red",
+  palettes = list(
+    species = c(Chinstrap = "#C55BCC", Adelie = "#FF7F02", Gentoo = "#047476"),
+    sex = c(male = "#0072B2", female = "#CC79A7"),
+    island = c(Biscoe = "#E69F00", Dream = "#56B4E9", Torgersen = "#009E73")
+    )
+)
+
+figure1c
+
+ggsaves::ggisaves(figure1c, prefix = "figure1c", outfolder = here("paper/"), dpi = 300, title = "PalmerPenguins")
+```
+
+## Figure 2
+
+```{r, fig.height = 4, fig.width = 16}
+figure2a <- gg1d(
+    lazy_birdwatcher,
+    col_sort = "Magpies", 
+    show_legend = TRUE,
+    fontsize_y_text = 24,
+    fontsize_barplot_y_numbers = 20, 
+    legend_text_size = 24, 
+    legend_key_size = 1.2,
+    legend_nrow = 1, 
+    na_marker_size = 14,
+    palettes = list(
+        Birdwatcher = c(Robert = "#E69F00", Catherine = "#999999"),
+        Day = c(Weekday = "#999999" ,Weekend = "#009E73")
+    ), interactive_svg_height = 4, interactive_svg_width = 16
+)
+
+figure2a
+
+ggsaves::ggisaves(figure2a, prefix = "figure2a", outfolder = here("paper/"), dpi = 300, title = "Lazy Birdwatcher")
+```
+
+```{r, fig.height=4, fig.width=5}
+library(GGally)
+figure2b <- ggpairs(lazy_birdwatcher, mapping = aes(color=Day)) + ggplot2::theme_bw() + scale_fill_manual(values = c(Weekday = "#999999" ,Weekend = "#009E73"))
+
+figure2b
+
+ggsaves::ggsaves(
+  figure2b, 
+  prefix = "figure2b", outfolder = here("paper/"), 
+  dpi = 300, height = 4, width = 5
+  )
+```
+
+```{r, fig.height=4, fig.width=5}
+library(skimr)
+figure2c <- skim(lazy_birdwatcher)
+
+figure2c
+
+
+# ggsaves::ggsaves(
+#   figure2b, 
+#   prefix = "figure2c", outfolder = here("paper/"), 
+#   dpi = 300, height = 4, width = 5
+#   )
+```
+
+## Table 1
+
+```{r}
+library(DataExplorer)
+create_report(lazy_birdwatcher)
+```
+
+## Figure 3
+
+UMAP + Iris
+
+```{r}
+library(uwot)
+umap(iris[1:4])
+
+```