Order legend in a R Plotly Bubblemap following factor order - r

I'm working on a Bubble map where I generated two columns, one for a color id (column Color) and one for a text refering to the id (column Class). This is a classification of my individuals (Color always belongs to Class).
Class is a factor following a certain order that I made with :
COME1039$Class <- as.factor(COME1039$Class, levels = c('moins de 100 000 F.CFP',
'entre 100 000 et 5 millions F.CFP',
'entre 5 millions et 1 milliard F.CFP',
'entre 1 milliard et 20 milliards F.CFP',
'plus de 20 milliards F.CFP'))
This is my code
g <- list(
scope = 'world',
visible = F,
showland = TRUE,
landcolor = toRGB("#EAECEE"),
showcountries = T,
countrycolor = toRGB("#D6DBDF"),
showocean = T,
oceancolor = toRGB("#808B96")
)
COM.g1 <- plot_geo(data = COME1039,
sizes = c(1, 700))
COM.g1 <- COM.g1 %>% add_markers(
x = ~LONGITUDE,
y = ~LATITUDE,
name = ~Class,
size = ~`Poids Imports`,
color = ~Color,
colors=c(ispfPalette[c(1,2,3,7,6)]),
text=sprintf("<b>%s</b> <br>Poids imports: %s tonnes<br>Valeur imports: %s millions de F.CFP",
COME1039$NomISO,
formatC(COME1039$`Poids Imports`/1000,
small.interval = ",",
digits = 1,
big.mark = " ",
decimal.mark = ",",
format = "f"),
formatC(COME1039$`Valeur Imports`/1000000,
small.interval = ",",
digits = 1,
big.mark = " ",
decimal.mark = ",",
format = "f")),
hovertemplate = "%{text}<extra></extra>"
)
COM.g1 <- COM.g1%>% layout(geo=g)
COM.g1 <- COM.g1%>% layout(dragmode=F)
COM.g1 <- COM.g1 %>% layout(showlegend=T)
COM.g1 <- COM.g1 %>% layout(legend = list(title=list(text='Valeurs des importations<br>'),
orientation = "h",
itemsizing='constant',
x=0,
y=0)) %>% hide_colorbar()
COM.g1
Unfortunately my data are too big to be added here, but this is the output I get :
As you can see, the order of the legend is not the one of the factor levels. How to get it ? If data are mandatory to help you to give me a hint, I will try to limit their size.
Many thanks !

Plotly is going to alphabetize your legend and you have to 'make' it listen. The order of the traces in your plot is the order in which the items appear in your legend. So if you rearrange the traces in the object, you'll rearrange the legend.
I don't have your data, so I used some data from rnaturalearth.
First I created a plot, using plot_geo. Then I used plotly_build() to make sure I had the trace order in the Plotly object. I used lapply to investigate the current order of the traces. Then I created a new order, rearranged the traces, and plotted it again.
The initial plot and build.
library(tidyverse)
library(plotly)
library(rnaturalearth)
canada <- ne_states(country = "Canada", returnclass = "SF")
x = plot_geo(canada, sizes = c(1, 700)) %>%
add_markers(x = ~longitude, y = ~latitude,
name = ~name, color = ~name)
x <- plotly_build(x) # capture all elements of the object
Now for the investigation; this is more so you can see how this all comes together.
# what order are they in?
y = vector()
invisible(
lapply(1:length(x$x$data),
function(i) {
z <- x$x$data[[i]]$name
message(i, " ", z)
})
)
# 1 Alberta
# 2 British Columbia
# 3 Manitoba
# 4 New Brunswick
# 5 Newfoundland and Labrador
# 6 Northwest Territories
# 7 Nova Scotia
# 8 Nunavut
# 9 Ontario
# 10 Prince Edward Island
# 11 Québec
# 12 Saskatchewan
# 13 Yukon
In your question, you show that you made the legend element a factor. That's what I've done as well with this data.
can2 = canada %>%
mutate(name = ordered(name,
levels = c("Manitoba", "New Brunswick",
"Newfoundland and Labrador",
"Northwest Territories",
"Alberta", "British Columbia",
"Nova Scotia", "Nunavut",
"Ontario", "Prince Edward Island",
"Québec", "Saskatchewan", "Yukon")))
I used the data to reorder the traces in my Plotly object. This creates a vector. It starts with the levels and their row number or order (1:13). Then I alphabetized the data by the levels (so it matches the current order in the Plotly object).
The output of this set of function calls is a vector of numbers (i.e., 5, 6, 1, etc.). Since I have 13 names, I have 1:13. You could always make it dynamic, as well 1:length(levels(can2$name).
# capture order
df1 = data.frame(who = levels(can2$name), ord = 1:13) %>%
arrange(who) %>% select(ord) %>% unlist()
Now all that's left is to rearrange the object traces and visualize it.
x$x$data = x$x$data[order(c(df1))] # reorder the traces
x # visualize
Originally:
With reordered traces:

Related

Colour specific countries on a worldmap and adding mappoint cities

I want to design a worldmap to show from which country and which city the participants to my survey come from. I used the highcharter package.
First part is : colour the countries --> it worked well ! A scale is created from 0 to 1.
Second part is : adding the cities --> the points are created but the countries colored in blue disappeared ! The scale has changed and is now induced from cities.
I try to change the order of my code but nothing is working.
library(dplyr)
library(maps)
library(magrittr)
# I use the dataset called iso3166 from the {maps} package and rename it date
dat <- iso3166
head(dat)
# I rename the variable a3 by iso-a3
dat <- rename(dat, "iso-a3" = a3)
head(dat)
# I create a vector with the countries I want to colour
part1X_countries <- c("CHE", "FRA", "USA", "GBR", "CAN", "BRA")
dat$part1X <- ifelse(dat$`iso-a3` %in% part1X_countries, 1, 0)
head(dat)
# I add the name of cities with geographical coordinates
cities <- data.frame(
name = c("St Gallen", "Fort Lauderdale", "Paris", "Nottingham", "Winnipeg", "Chicago", "Leeds", "Montréal", "New Rochelle", "São Paulo", "Saint-Genis-Pouilly", "Canterbury"),
lat = c(47.42391, 26.122438, 48.866667, 52.950001, 49.8955, 41.881832, 53.801277, 45.5016889, 40.9232, -23.5489, 46.24356, 51.279999),
lon = c(9.37477, -80.137314, 2.333333, -1.150000, -97.1383, -87.623177, -1.548567, -73.567256, -73.7793, -46.6388, 6.02119, 1.080000))
# I create my worldmap with countries and cities
worldmap <- hcmap(
map = "custom/world-highres3", # high resolution world map
data = dat, # name of dataset
value = "part1X",
joinBy = "iso-a3",
showInLegend = FALSE, # hide legend
download_map_data = TRUE
) %>%
hc_add_series(
data = cities,
type = "mappoint",
name = "Cities"
) %>%
hc_title(text = "Representation of participants by country")```
You need to define a colorkey and add a color axis for the hcmap. The below code keeps the colors from the countries and has the name of the countries added on top as black map points.
worldmap <- hcmap(
map = "custom/world-highres3", # high resolution world map
data = dat, # name of dataset
value = "part1X",
joinBy = "iso-a3",
colorKey = "value",
showInLegend = F, # hide legend
download_map_data = TRUE) %>%
hc_colorAxis(min = min(dat$part1X),
max = max(dat$part1X)) %>%
hc_add_series(
data = cities,
type = "mappoint",
name = "Cities",
dataLabels = list(enabled = TRUE, format = '{point.name}'),
latField = "lat",
longField = "lon",
# color = "color"
valueField = "part1X"
) %>%
hc_title(text = "Representation of participants by country")
worldmap

Order by name if repeat

I would like to sort the bars in descending order by value and if the value is repeated the name of the city must appear in alphabetical order
library(plotly)
city <- c("Paris", "New York", "Rio", "Salvador", "Curitiba", "Natal")
value <- c(10,20,30,10,10,10)
data <- data.frame(city, value, stringsAsFactors = FALSE)
data$city <- factor(data$city, levels = unique(data$city)[order(data$value, decreasing = FALSE)])
fig <- plot_ly(y = data$city, x = data$value, type = "bar", orientation = 'h')
Can be achieved using order function on dataframe. Applies order on value column, (-) sign indicates decreasing, and then on city name
data_ordered <- data[order(-data$value, data$city),]
data_ordered
city value
3 Rio 30
2 New York 20
5 Curitiba 10
6 Natal 10
1 Paris 10
4 Salvador 10
data_ordered$city <- factor(data_ordered$city, levels = data_ordered$city)
plot_ly(y = data_ordered$city, x = data_ordered$value, type = "bar", orientation = 'h') %>%
layout(yaxis = list(autorange = "reversed"))
Using tidyverse, i suggest that :
library(tidyverse)
city <- c("Paris", "New York", "Rio", "Salvador", "Curitiba", "Natal")
value <- c(10,20,30,10,10,10)
data <- data.frame(city, value)
db <- as_tibble(data)
db %>%
ggplot(aes(x = reorder(city, -value), y=value))+
geom_col()
The "reorder" function in the definition of "x" make what you want, and the alphabetical order is respected.
To make this graph vertically, add coord_flip in the end.
The "-value" can be switch to "value" if you want reorder
library(tidyverse)
city <- c("Paris", "New York", "Rio", "Salvador", "Curitiba", "Natal", "Zoo", "Aaa")
value <- c(10,20,30,10,10,10,10,10)
data <- data.frame(city, value)
db <- as_tibble(data)
db %>%
ggplot(aes(x = reorder(city, value), y=value))+
geom_col() +
coord_flip()

Drawing arbitrary lines on a highchart map in R (library highcharter)

I am drawing a highcharts map using the highcharter package in R. I added already some points (cities) and want to link them by drawing an additionnal beeline using the world map-coordinates.
I already managed to draw the beelines by first drawing the map, then hovering over the cities which shows me the plot-coordinates, and then redrawing the plot using the aforementioned plot-coordinates. (Watch out: I used the PLOT-coordinates and my goal is to use directly the WORLD MAP-coordinates.)
If you only have 1 or two cities, it's not a big deal. But if you have like 100 cities/points, it's annoying. I guess the answer will be something like here: Is it possible to include maplines in highcharter maps?.
Thank you!
Here my code:
library(highcharter)
library(tidyverse)
# cities with world coordinates
ca_cities <- data.frame(
name = c("San Diego", "Los Angeles", "San Francisco"),
lat = c(32.715736, 34.052235, 37.773972), # world-map-coordinates
lon = c(-117.161087, -118.243683, -122.431297) # world-map-coordinates
)
# path which I create AFTER the first drawing of the map as I get the
# plot-coordinates when I hover over the cities.
path <- "M669.63,-4963.70,4577.18,-709.5,5664.42,791.88"
# The goal: the path variable above should be defined using the WORLD-
# coordinates in ca_cities and not using the PLOT-coordinates.
# information for drawing the beeline
ca_lines <- data.frame(
name = "line",
path = path,
lineWidth = 2
)
# construct the map
map <- hcmap("countries/us/us-ca-all", showInLegend = FALSE) %>%
hc_add_series(data = ca_cities, type = "mappoint", name = "Cities") %>%
hc_add_series(data = ca_lines, type = "mapline", name = "Beeline", color = "blue")
map
See picture here
After several hours, I found an answer to my problem. There are maybe easier ways, but I'm going to post my version using the rgdal-package.
The idea is to convert first the world map-coordinates to the specific map's coordinate system (ESRI) and then back-transform all adjustments from highcharts:
library(highcharter)
library(tidyverse)
library(rgdal) # you also need rgdal
# cities with world coordinates
ca_cities <- data.frame(
name = c("San Diego", "Los Angeles", "San Francisco"),
lat = c(32.715736, 34.052235, 37.773972),
lon = c(-117.161087, -118.243683, -122.431297)
)
# pre-construct the map
map <- hcmap("countries/us/us-ca-all", showInLegend = FALSE)
# extract the transformation-info
trafo <- map$x$hc_opts$series[[1]]$mapData$`hc-transform`$default
# convert to coordinates
ca_cities2 <- ca_cities %>% select("lat", "lon")
coordinates(ca_cities2) <- c("lon", "lat")
# convert world geosystem WGS 84 into transformed crs
proj4string(ca_cities2) <- CRS("+init=epsg:4326") # WGS 84
ca_cities3 <- spTransform(ca_cities2, CRS(trafo$crs)) #
# re-transform coordinates according to the additionnal highcharts-parameters
image_coords_x <- (ca_cities3$lon - trafo$xoffset) * trafo$scale * trafo$jsonres + trafo$jsonmarginX
image_coords_y <- -((ca_cities3$lat - trafo$yoffset) * trafo$scale * trafo$jsonres + trafo$jsonmarginY)
# construct the path
path <- paste("M",
paste0(paste(image_coords_x, ",", sep = ""),
image_coords_y, collapse = ","),
sep = "")
# information for drawing the beeline
ca_lines <- data.frame(
name = "line",
path = path,
lineWidth = 2
)
# add series
map <- map %>%
hc_add_series(data = ca_cities, type = "mappoint", name = "Cities") %>%
hc_add_series(data = ca_lines, type = "mapline", name = "Beeline", color = "blue")
map

how to plot networks over a map with the least overlap

I have some authors with their city or country of affiliation. I would like to know if it is possible to plot the coauthors' networks (figure 1), on the map, having the coordinates of the countries. Please consider multiple authors from the same country. [EDIT: Several networks could be generated as in the example and should not show avoidable overlaps]. This is intended for dozens of authors. A zooming option is desirable. Bounty promise +100 for future better answer.
refs5 <- read.table(text="
row bibtype year volume number pages title journal author
Bennett_1995 article 1995 76 <NA> 113--176 angiosperms. \"Annals of Botany\" \"Bennett Md, Leitch Ij\"
Bennett_1997 article 1997 80 2 169--196 estimates. \"Annals of Botany\" \"Bennett MD, Leitch IJ\"
Bennett_1998 article 1998 82 SUPPL.A 121--134 weeds. \"Annals of Botany\" \"Bennett MD, Leitch IJ, Hanson L\"
Bennett_2000 article 2000 82 SUPPL.A 121--134 weeds. \"Annals of Botany\" \"Bennett MD, Someone IJ\"
Leitch_2001 article 2001 83 SUPPL.A 121--134 weeds. \"Annals of Botany\" \"Leitch IJ, Someone IJ\"
New_2002 article 2002 84 SUPPL.A 121--134 weeds. \"Annals of Botany\" \"New IJ, Else IJ\"" , header=TRUE,stringsAsFactors=FALSE)
rownames(refs5) <- refs5[,1]
refs5<-refs5[,2:9]
citations <- as.BibEntry(refs5)
authorsl <- lapply(citations, function(x) as.character(toupper(x$author)))
unique.authorsl<-unique(unlist(authorsl))
coauth.table <- matrix(nrow=length(unique.authorsl),
ncol = length(unique.authorsl),
dimnames = list(unique.authorsl, unique.authorsl), 0)
for(i in 1:length(citations)){
paper.auth <- unlist(authorsl[[i]])
coauth.table[paper.auth,paper.auth] <- coauth.table[paper.auth,paper.auth] + 1
}
coauth.table <- coauth.table[rowSums(coauth.table)>0, colSums(coauth.table)>0]
diag(coauth.table) <- 0
coauthors<-coauth.table
bip = network(coauthors,
matrix.type = "adjacency",
ignore.eval = FALSE,
names.eval = "weights")
authorcountry <- read.table(text="
author country
1 \"LEITCH IJ\" Argentina
2 \"HANSON L\" USA
3 \"BENNETT MD\" Brazil
4 \"SOMEONE IJ\" Brazil
5 \"NEW IJ\" Brazil
6 \"ELSE IJ\" Brazil",header=TRUE,fill=TRUE,stringsAsFactors=FALSE)
matched<- authorcountry$country[match(unique.authorsl, authorcountry$author)]
bip %v% "Country" = matched
colorsmanual<-c("red","darkgray","gainsboro")
names(colorsmanual) <- unique(matched)
gdata<- ggnet2(bip, color = "Country", palette = colorsmanual, legend.position = "right",label = TRUE,
alpha = 0.9, label.size = 3, edge.size="weights",
size="degree", size.legend="Degree Centrality") + theme(legend.box = "horizontal")
gdata
In other words, adding the names of authors, lines and bubbles to the map. Note, several authors maybe from the same city, or country and should not overlap.
Figure 1 Network
EDIT: The current JanLauGe answer overlaps two non-related networks. authors "ELSE" and "NEW" need to be apart from others as in figure 1.
Are you looking for a solution using exactly the packages you used, or would you be happy to use suite of other packages? Below is my approach, in which I extract the graph properties from the network object and plot them on a map using the ggplot2 and map package.
First I recreate the example data you gave.
library(tidyverse)
library(sna)
library(maps)
library(ggrepel)
set.seed(1)
coauthors <- matrix(
c(0,3,1,1,3,0,1,0,1,1,0,0,1,0,0,0),
nrow = 4, ncol = 4,
dimnames = list(c('BENNETT MD', 'LEITCH IJ', 'HANSON L', 'SOMEONE ELSE'),
c('BENNETT MD', 'LEITCH IJ', 'HANSON L', 'SOMEONE ELSE')))
coords <- data_frame(
country = c('Argentina', 'Brazil', 'USA'),
coord_lon = c(-63.61667, -51.92528, -95.71289),
coord_lat = c(-38.41610, -14.23500, 37.09024))
authorcountry <- data_frame(
author = c('LEITCH IJ', 'HANSON L', 'BENNETT MD', 'SOMEONE ELSE'),
country = c('Argentina', 'USA', 'Brazil', 'Brazil'))
Now I generate the graph object using the snp function network
# Generate network
bip <- network(coauthors,
matrix.type = "adjacency",
ignore.eval = FALSE,
names.eval = "weights")
# Graph with ggnet2 for centrality
gdata <- ggnet2(bip, color = "Country", legend.position = "right",label = TRUE,
alpha = 0.9, label.size = 3, edge.size="weights",
size="degree", size.legend="Degree Centrality") + theme(legend.box = "horizontal")
From the network object we can extract the values of each edge, and from the ggnet2 object we can get degree of centrality for nodes as below:
# Combine data
authors <-
# Get author numbers
data_frame(
id = seq(1, nrow(coauthors)),
author = sapply(bip$val, function(x) x$vertex.names)) %>%
left_join(
authorcountry,
by = 'author') %>%
left_join(
coords,
by = 'country') %>%
# Jittering points to avoid overlap between two authors
mutate(
coord_lon = jitter(coord_lon, factor = 1),
coord_lat = jitter(coord_lat, factor = 1))
# Get edges from network
networkdata <- sapply(bip$mel, function(x)
c('id_inl' = x$inl, 'id_outl' = x$outl, 'weight' = x$atl$weights)) %>%
t %>% as_data_frame
dt <- networkdata %>%
left_join(authors, by = c('id_inl' = 'id')) %>%
left_join(authors, by = c('id_outl' = 'id'), suffix = c('.from', '.to')) %>%
left_join(gdata$data %>% select(label, size), by = c('author.from' = 'label')) %>%
mutate(edge_id = seq(1, nrow(.)),
from_author = author.from,
from_coord_lon = coord_lon.from,
from_coord_lat = coord_lat.from,
from_country = country.from,
from_size = size,
to_author = author.to,
to_coord_lon = coord_lon.to,
to_coord_lat = coord_lat.to,
to_country = country.to) %>%
select(edge_id, starts_with('from'), starts_with('to'), weight)
Should look like this now:
dt
# A tibble: 8 × 11
edge_id from_author from_coord_lon from_coord_lat from_country from_size to_author to_coord_lon
<int> <chr> <dbl> <dbl> <chr> <dbl> <chr> <dbl>
1 1 BENNETT MD -51.12756 -16.992729 Brazil 6 LEITCH IJ -65.02949
2 2 BENNETT MD -51.12756 -16.992729 Brazil 6 HANSON L -96.37907
3 3 BENNETT MD -51.12756 -16.992729 Brazil 6 SOMEONE ELSE -52.54160
4 4 LEITCH IJ -65.02949 -35.214117 Argentina 4 BENNETT MD -51.12756
5 5 LEITCH IJ -65.02949 -35.214117 Argentina 4 HANSON L -96.37907
6 6 HANSON L -96.37907 36.252312 USA 4 BENNETT MD -51.12756
7 7 HANSON L -96.37907 36.252312 USA 4 LEITCH IJ -65.02949
8 8 SOMEONE ELSE -52.54160 -9.551913 Brazil 2 BENNETT MD -51.12756
# ... with 3 more variables: to_coord_lat <dbl>, to_country <chr>, weight <dbl>
Now moving on to plotting this data on a map:
world_map <- map_data('world')
myMap <- ggplot() +
# Plot map
geom_map(data = world_map, map = world_map, aes(map_id = region),
color = 'gray85',
fill = 'gray93') +
xlim(c(-120, -20)) + ylim(c(-50, 50)) +
# Plot edges
geom_segment(data = dt,
alpha = 0.5,
color = "dodgerblue1",
aes(x = from_coord_lon, y = from_coord_lat,
xend = to_coord_lon, yend = to_coord_lat,
size = weight)) +
scale_size(range = c(1,3)) +
# Plot nodes
geom_point(data = dt,
aes(x = from_coord_lon,
y = from_coord_lat,
size = from_size,
colour = from_country)) +
# Plot names
geom_text_repel(data = dt %>%
select(from_author,
from_coord_lon,
from_coord_lat) %>%
unique,
colour = 'dodgerblue1',
aes(x = from_coord_lon, y = from_coord_lat, label = from_author)) +
coord_equal() +
theme_bw()
Obviously you can change the colour and design in the usual way with ggplot2 grammar. Notice that you could also use geom_curve and the arrow aesthetic to get a plot similar to the one in the uber post linked in the comments above.
As an effort to avoid the overlapping of the 2 networks, I came to this modification of the x and y coordenates of the ggplot, which by default does not overlap the networks, see figure 1 in the question.
# get centroid positions for countries
# add coordenates to authorcountry table
# download and unzip
# https://worldmap.harvard.edu/data/geonode:country_centroids_az8
setwd("~/country_centroids_az8")
library(rgdal)
cent <- readOGR('.', "country_centroids_az8", stringsAsFactors = F)
countrycentdf<-cent#data[,c("name","Longitude","Latitude")]
countrycentdf$name[which(countrycentdf$name=="United States")]<-"USA"
colnames(countrycentdf)[names(countrycentdf)=="name"]<-"country"
authorcountry$Longitude<-countrycentdf$Longitude[match(authorcountry$country,countrycentdf$country)]
authorcountry$Latitude <-countrycentdf$Latitude [match(authorcountry$country,countrycentdf$country)]
# original coordenates of plot and its transformation
ggnetbuild<-ggplot_build(gdata)
allcoord<-ggnetbuild$data[[3]][,c("x","y","label")]
allcoord$Latitude<-authorcountry$Latitude [match(allcoord$label,authorcountry$author)]
allcoord$Longitude<-authorcountry$Longitude [match(allcoord$label,authorcountry$author)]
allcoord$country<-authorcountry$country [match(allcoord$label,authorcountry$author)]
# increase with factor the distance among dots
factor<-7
allcoord$coord_lat<-allcoord$y*factor+allcoord$Latitude
allcoord$coord_lon<-allcoord$x*factor+allcoord$Longitude
allcoord$author<-allcoord$label
# plot as in answer of JanLauGe, without jitter
library(tidyverse)
library(ggrepel)
authors <-
# Get author numbers
data_frame(
id = seq(1, nrow(coauthors)),
author = sapply(bip$val, function(x) x$vertex.names)) %>%
left_join(
allcoord,
by = 'author')
# Continue as in answer of JanLauGe
networkdata <- ##
dt <- ##
world_map <- map_data('world')
myMap <- ##
myMap

Using R plotly to produce a windrose chart

I am aiming to produce a Wind Rose chart using plotly that plots a country's (SG) rating for 5 variables (X1, X2, X3, X4, X5).
Reproducible Code
library(plotly) # viz
library(tidyr) # data munge
library(dplyr) # data munge
# list of countries
Countries <- c("SG", "UK", "CAD", "USA", "AU")
# data
set.seed(1)
data.frame(replicate(5, sample(0:10, 5, rep=TRUE))) %>%
cbind(Countries) %>%
gather(key = Variable
, value = value
, -Countries) ->
df
# single country
SG <- df[df$Countries %in% c("SG"),]
# plot
plot_ly(SG
, r = value #radial
, t = Variable #angular coordinates
, color = Variable
, type = "area") %>%
layout(radialaxis = list(ticksuffix = "pts")
, orientation = 270
, autosize = T
, width = 500
, height = 500
, margin = list(l = 100
, r = 50
, b = 100
, t = 50
, pad = 0
, autoexpand=FALSE)) %>%
config(displayModeBar = F, showLink = F) ->
p
p
The Issue
Currently I get a blank canvas (see screenshot):
UPDATE
A further point to note per #MLavoie's comment, is that the plot is not a blank canvas when you plot df (see screenshot 2 below). However, it doesn't seem to reflect the input data. Eg. variable X1 in the plot has a value of 8 whereas the data has a value of sum(df[df$Variable == "X1", "value"]) = 23.

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