296 lines
10 KiB
Text
296 lines
10 KiB
Text
---
|
|
output: github_document
|
|
---
|
|
|
|
<!-- README.md is generated from README.Rmd. Please edit that file -->
|
|
|
|
```{r, include = FALSE}
|
|
knitr::opts_chunk$set(
|
|
collapse = TRUE,
|
|
comment = "#>",
|
|
fig.path = "man/figures/README-",
|
|
out.width = "100%",
|
|
warning = FALSE,
|
|
message = FALSE,
|
|
dpi = 300,
|
|
dev.args = list(type = "cairo")
|
|
)
|
|
|
|
desc = read.dcf('DESCRIPTION')
|
|
desc = setNames(as.list(desc), colnames(desc))
|
|
```
|
|
|
|
# `r desc$Package` <img src="man/figures/logo.png" align="right" alt="" width="120"/>
|
|
|
|
> `r desc$Title`
|
|
|
|
`visualizeR` proposes some utils to get REACH and AGORA colors, ready-to-go color palettes, and a few visualization functions (horizontal hist graph for instance).
|
|
|
|
## Installation
|
|
|
|
You can install the last version of visualizeR from
|
|
[GitHub](https://github.com/) with:
|
|
|
|
```{r, eval = FALSE}
|
|
# install.packages("devtools")
|
|
devtools::install_github("gnoblet/visualizeR", build_vignettes = TRUE)
|
|
```
|
|
|
|
## Roadmap
|
|
|
|
Roadmap is as follows:
|
|
|
|
- [X] Add IMPACT's colors
|
|
- [X] Add all color palettes from the internal documentation
|
|
- [ ] There remains to be added more-than-7-color palettes and black color palettes
|
|
- [X] Add new types of visualization (e.g. dumbbell plot, lollipop plot, etc.)
|
|
- [X] Use examples
|
|
- [ ] Add some ease-map functions
|
|
- [ ] Add some interactive functions (maps and graphs)
|
|
- [ ] Consolidate and make errors transparent
|
|
|
|
## Request
|
|
|
|
Please, do not hesitate to pull request any new viz or colors or color palettes, or to email request any change (guillaume.noblet@reach-initiative.org or gnoblet@zaclys.net).
|
|
|
|
## Colors
|
|
|
|
Color palettes for REACH, AGORA and IMPACT are available. Functions to access colors and palettes are `cols_initiative()` or `pal_initiative()`. For now, the initiative with the most colors and color palettes is REACH. Feel free to pull requests new AGORA and IMPACT colors.
|
|
|
|
```{r example-colors, eval = TRUE}
|
|
library(visualizeR)
|
|
|
|
# Get all saved REACH colors, named
|
|
cols_reach(unnamed = F)[1:10]
|
|
|
|
# Extract a color palette as hexadecimal codes and reversed
|
|
pal_reach(palette = "main", reversed = TRUE, color_ramp_palette = FALSE)
|
|
|
|
# Get all color palettes names
|
|
pal_reach(show_palettes = T)
|
|
```
|
|
|
|
## Charts
|
|
|
|
### Example 1: Bar chart, already REACH themed
|
|
|
|
```{r example-bar-chart, out.width = "65%", eval = TRUE}
|
|
library(visualizeR)
|
|
library(palmerpenguins)
|
|
library(dplyr)
|
|
|
|
df <- penguins |>
|
|
group_by(island, species) |>
|
|
summarize(
|
|
mean_bl = mean(bill_length_mm, na.rm = T),
|
|
mean_fl = mean(flipper_length_mm, na.rm = T)) |>
|
|
ungroup()
|
|
|
|
# Simple bar chart by group with some alpha transparency
|
|
bar(df, island, mean_bl, species, percent = FALSE, alpha = 0.6, x_title = "Mean of bill length")
|
|
|
|
# Using another color palette through `theme_reach()` and changing scale to percent
|
|
bar(df, island,mean_bl, species, percent = TRUE, theme = theme_reach(palette = "artichoke_3"))
|
|
|
|
# Not flipped, with text added, group_title, no y-axis and no bold for legend
|
|
bar(df, island, mean_bl, species, group_title = "Species", flip = FALSE, add_text = TRUE, add_text_suffix = "%", percent = FALSE, theme = theme_reach(text_font_face = "plain", axis_y = FALSE))
|
|
|
|
```
|
|
|
|
### Example 2: Point chart, already REACH themed
|
|
|
|
At this stage, `point_reach()` only supports categorical grouping colors with the `group` arg.
|
|
|
|
```{r example-point-chart, out.width = "65%", eval = TRUE}
|
|
|
|
# Simple point chart
|
|
point(penguins, bill_length_mm, flipper_length_mm)
|
|
|
|
# Point chart with grouping colors, greater dot size, some transparency, reversed color palette
|
|
point(penguins, bill_length_mm, flipper_length_mm, island, alpha = 0.6, size = 3, theme = theme_reach(reverse = TRUE))
|
|
|
|
# Using another color palettes
|
|
point(penguins, bill_length_mm, flipper_length_mm, island, size = 1.5, x_title = "Bill", y_title = "Flipper", title = "Length (mm)", theme = theme_reach(palette = "artichoke_3", text_font_face = , grid_major_x = TRUE, title_position_to_plot = FALSE))
|
|
```
|
|
|
|
|
|
### Example 3: Dumbbell plot, REACH themed
|
|
|
|
Remember to ensure that your data are in the long format and you only have two groups on the x-axis; for instance, IDP and returnee and no NA values.
|
|
|
|
```{r example-dumbbell-plot, out.width = "65%", eval = TRUE}
|
|
# Prepare long data
|
|
df <- tibble::tibble(
|
|
admin1 = rep(letters[1:8], 2),
|
|
setting = c(rep(c("Rural", "Urban"), 4), rep(c("Urban", "Rural"), 4)),
|
|
stat = rnorm(16, mean = 50, sd = 18)
|
|
) |>
|
|
dplyr::mutate(stat = round(stat, 0))
|
|
|
|
# Example, adding a parameter to `theme_reach()` passed on `ggplot2::theme()` to align legend title
|
|
dumbbell(df,
|
|
stat,
|
|
setting,
|
|
admin1,
|
|
title = "% of HHs that reported open defecation as sanitation facility",
|
|
group_y_title = "Admin 1",
|
|
group_x_title = "Setting",
|
|
theme = theme_reach(legend_position = "bottom",
|
|
legend_direction = "horizontal",
|
|
legend_title_font_face = "bold",
|
|
palette = "primary",
|
|
title_position_to_plot = FALSE,
|
|
legend.title.align = 0.5)) +
|
|
# Change legend title position (could be included as part of the function)
|
|
ggplot2::guides(
|
|
color = ggplot2::guide_legend(title.position = "left"),
|
|
fill = ggplot2::guide_legend(title.position = "left")
|
|
)
|
|
```
|
|
|
|
### Example 4: donut chart, REACH themed (to used once, not twice)
|
|
```{r example-donut-plot, out.width = "65%", warning = FALSE}
|
|
|
|
# Some summarized data: % of HHs by displacement status
|
|
df <- tibble::tibble(
|
|
status = c("Displaced", "Non displaced", "Returnee", "Don't know/Prefer not to say"),
|
|
percentage = c(18, 65, 12, 3)
|
|
)
|
|
|
|
# Donut
|
|
donut(df,
|
|
status,
|
|
percentage,
|
|
hole_size = 3,
|
|
add_text_suffix = "%",
|
|
add_text_color = cols_reach("dk_grey"),
|
|
add_text_treshold_display = 5,
|
|
x_title = "Displacement status",
|
|
title = "% of HHs by displacement status",
|
|
theme = theme_reach(legend_reverse = TRUE))
|
|
```
|
|
|
|
### Example 4: donut chart, REACH themed (to used once, not twice)
|
|
```{r example-donut-plot, out.width = "65%", warning = FALSE}
|
|
|
|
# Donut
|
|
waffle(df,
|
|
status,
|
|
percentage,
|
|
title = "% of HHs by displacement status",
|
|
theme = theme_reach(legend_reverse = TRUE))
|
|
```
|
|
|
|
### Example 5: alluvial chart, REACH themed
|
|
```{r example-alluvial-plot, out.width = "65%", warning = FALSE}
|
|
|
|
# Some summarized data: % of HHs by self-reported status of displacement in 2021 and in 2022
|
|
df <- tibble::tibble(
|
|
status_from = c(rep("Displaced", 4),
|
|
rep("Non displaced", 4),
|
|
rep("Returnee", 4),
|
|
rep("Dnk/Pnts", 4)),
|
|
status_to = c("Displaced", "Non displaced", "Returnee", "Dnk/Pnts", "Displaced", "Non displaced", "Returnee", "Dnk/Pnts", "Displaced", "Non displaced", "Returnee", "Dnk/Pnts", "Displaced", "Non displaced", "Returnee", "Dnk/Pnts"),
|
|
percentage = c(20, 8, 18, 1, 12, 21, 0, 2, 0, 3, 12, 1, 0, 0, 1, 1)
|
|
)
|
|
|
|
# Alluvial, here the group is the status for 2021
|
|
|
|
alluvial(df,
|
|
status_from,
|
|
status_to,
|
|
percentage,
|
|
status_from,
|
|
from_levels = c("Displaced", "Non displaced", "Returnee", "Dnk/Pnts"),
|
|
alpha = 0.8,
|
|
group_title = "Status for 2021",
|
|
title = "% of HHs by self-reported status from 2021 to 2022",
|
|
theme = theme_reach(
|
|
axis_y = FALSE,
|
|
legend_position = "none"))
|
|
|
|
```
|
|
|
|
### Example 6: lollipop chart
|
|
```{r example-lollipop-chart, out.width = "65%", warning = FALSE}
|
|
library(tidyr)
|
|
# Prepare long data
|
|
df <- tibble::tibble(
|
|
admin1 = replicate(15, sample(letters, 8)) |> t() |> as.data.frame() |> unite("admin1", sep = "") |> dplyr::pull(admin1),
|
|
stat = rnorm(15, mean = 50, sd = 15)) |>
|
|
dplyr::mutate(stat = round(stat, 0))
|
|
|
|
# Make lollipop plot, REACH themed, vertical with 45 degrees angle X-labels
|
|
lollipop(df,
|
|
admin1,
|
|
stat,
|
|
arrange = FALSE,
|
|
add_text = FALSE,
|
|
flip = FALSE,
|
|
y_title = "% of HHs",
|
|
x_title = "Admin 1",
|
|
title = "% of HHs that reported having received a humanitarian assistance",
|
|
theme = theme_reach(axis_text_x_angle = 45,
|
|
grid_major_y = TRUE,
|
|
grid_major_y_size = 0.2,
|
|
grid_major_x = TRUE,
|
|
grid_minor_y = TRUE))
|
|
|
|
# Horizontal, greater point size, arranged by value, no grid, and text labels added
|
|
lollipop(df,
|
|
admin1,
|
|
stat,
|
|
arrange = TRUE,
|
|
point_size = 10,
|
|
point_color = cols_reach("main_beige"),
|
|
segment_size = 2,
|
|
add_text = TRUE,
|
|
add_text_suffix = "%",
|
|
y_title = "% of HHs",
|
|
x_title = "Admin 1",
|
|
title = "% of HHs that reported having received a humanitarian assistance in the 12 months prior to the assessment",
|
|
theme = theme_reach(title_position_to_plot = FALSE))
|
|
|
|
|
|
```
|
|
|
|
|
|
## Maps
|
|
|
|
```{r example-map, out.width = "50%"}
|
|
|
|
# Add indicator layer
|
|
# - based on "pretty" classes and title "Proportion (%)"
|
|
# - buffer to add a 10% around the bounding box
|
|
map <- add_indicator_layer(
|
|
indicator_admin1,
|
|
opn_dfc,
|
|
buffer = 0.1) +
|
|
# Layout - some defaults - add the map title
|
|
add_layout("% of HH that reported open defecation as sanitation facility") +
|
|
# Admin boundaries as list of shape files (lines) and colors, line widths and labels as vectors
|
|
add_admin_boundaries(
|
|
lines = list(line_admin1, border_admin0, frontier_admin0),
|
|
colors = cols_reach("main_lt_grey", "dk_grey", "black"),
|
|
lwds = c(0.5, 2, 3),
|
|
labels = c("Department", "Country", "Dominican Rep. frontier"),
|
|
title = "Administrative boundaries") +
|
|
# Add text labels - centered on admin 1 centroids
|
|
add_admin_labels(centroid_admin1, ADM1_FR_UPPER) +
|
|
# Add a compass
|
|
add_compass() +
|
|
# Add a scale bar
|
|
add_scale_bar() +
|
|
# Add credits
|
|
add_credits("Admin. boundaries. : CNIGS \nCoord. system: GCS WGS 1984")
|
|
```
|
|
|
|
```{r map-save, eval = TRUE, include = FALSE, echo = TRUE}
|
|
tmap::tmap_save(map,
|
|
"man/figures/README-example-map.png",
|
|
height = 4.5,
|
|
width = 6
|
|
)
|
|
```
|
|
|
|
|