Points not added to the map plot

Question

I need to add some points to the map using simple points function. The issue is that points don't add to the map. It's simple command, I follow some tutorial where adding points to the map works this way but not in my case. Plot function plots Texas choropleth properly but next line ( points ) doesn't add points to the map at all:

library(rgdal)
library(rgeos)
library(sp)

companies <- read.csv('geoloc_data_comp.csv', header = T, dec = ',', sep = ';')
states <- readOGR('.', 'states')

plot(states[states@data$stat_name == 'texas',])
points(companies$coords.x1, companies$coords.x2, pch = 21)

Answer 1

First you shoud start to avoid rgeos / rgdal because they will stop being maintains. See: https://github.com/r-spatial/evolution

sf is replacing them:

library(sp)
library(sf)
library(spData) #used because I wanted US states
# list of data in spData you have one with US states
data(package = "spData")

if you want to read shapefile or other GIS format check sf::st_read() (instead of readOGR() )

# one way with sf
plot(us_states$geometry[us_states$NAME == "Texas"]) 
# if you want do use the sp way  
us_sp <- as(us_states, "Spatial") # convert to sp
plot(us_sp[us_sp@data$NAME == "Texas",])

with sf you have the geometry in one column (see "geometry") instead of having an R S4 with nested lists (see @data and @polygones).

Before getting some points we need to check in which CRS our data are. If you do not know CRS I like this website: https://ihatecoordinatesystems.com/

You also have information in the us_states documentation: https://www.rdocumentation.org/packages/spData/versions/2.0.1/topics/us_states

Then you can use:

sp::proj4string(us_sp)
sf::st_crs(us_states)
# This is EPSG 4269 or NAD83

If you want to use points() they need to be in this coordinates system ( I suspect this explain your trouble ie different CRS).

You didn't provide data points so I produced some:

library(osmdata)
#this will just download node matching the key/value place=city
some_city_in_texas <- osmdata::opq(osmdata::getbb("Texas US"),
                                   nodes_only = TRUE) %>% 
            osmdata::add_osm_feature(key = "place", value = "city") %>% 
            osmdata::osmdata_sf() #keep them in sf format 
                                  # osmdata_sp() also exist

The class osmdata is a bit complicated but here you just need to know that some_city_in_texas$osm_points provide us with points (to test points() ). Now we can check their CRS:

sf::st_crs(some_city_in_texas$osm_points)

As you can see we are in an other CRS so we need to transform it. (you will probably need to do it).

city_in_texas <- sf::st_transform(some_city_in_texas$osm_points,
                                  4269)

sf use simple feature standard to store localization and points() want two vectors x&y. You should also check that (common cause of error): R use x/y (long/lat) and not lat/long.

Here we convert city_in_texas to just coords. (if you need to do the reverse, ie converting data frame with X/Y, into an sf object look at sf::st_as_sf() )

coords_city <- sf::st_coordinates(city_in_texas)

Finally this works fine now:

plot(us_states$geometry[us_states$NAME == "Texas"]) 
points(coords_city, pch = 21)

Good ressources are https://r-spatial.org/ and https://geocompr.robinlovelace.net/