Clarke van Steenderen

Clarke van Steenderen

PhD student in the Department of Zoology and Entomology, Centre for Biological Control, Rhodes University

Creating an elevation map with GPS coordinate points

1 minute read

Published:

This R script plots the map of a desired country, and colours it by elevation. It then adds GPS coordinate points to it (for example sampling sites) from an Excel file. Check out the final image at the bottom of this post 😃. The North arrow and Tetramesa wasp was added manually later in Inkscape.


library(raster)
library(dplyr)
library(ggplot2)
library(readxl)
library(janitor)

getData("ISO3")

# Get data for South Africa
southafrica <- getData("alt", country="South Africa", mask = T)

# For some reason, the South Africa map doesn't save as a RasterLayer object, so run the equivalent of this line, changing the filepath appropriately to access the _msk_alt.grd file generated
southafrica_1 = southafrica$`C:/Users/s1000334/Documents/PhD_Tetramesa/R Scripts/map_plotting/ZAF1_msk_alt.grd`

# Check that it's a RasterLayer object
class(southafrica_1)

##################################
# Using base-R
##################################

# Quick peek at the map
plot(southafrica_1, main = "SA elevation", col = grey(1:100/100))

# Import GPS points from an Excel file on GitHub
sample_gps = readxl::read_xlsx("G:/My Drive/Tetramesa Project/Source Modifiers/source_modifiers_updated_10_06_2021.xlsx", sheet = "Tetramesa_Clarke")

# Apply some filtering specific to this Excel sheet
sample_gps = filter(sample_gps, mitochondrial_COI == "TRUE" | nuclear_28S == "TRUE")

# Check data import 
head(sample_gps)

# Clean the column names
sample_gps <- sample_gps %>%
  janitor::clean_names()

# Inspect the data
head(sample_gps)

# Generate the plot
plot( southafrica_1, main = "", col = grey(1:100/100), ylab = "Latitude", xlab = "Longitude" )
# If no colour is specified, the default palette used is rev(terrain.colors(255))
# E.g of a different coloured plot:
plot( southafrica_1, main = "", col = colorRampPalette(c("black", "orange"))( 255 ), ylab = "Latitude", xlab = "Longitude" )

# Add the GPS coordinates as red points
points(sample_gps$longitude, sample_gps$latitude, bg = "red", col = "black", pch = 21, cex = 2)

# Add a scalebar to the map
scalebar(d = 200, type = "bar", below = "km", xy=c(31,-34))

Multiple sequence alignment Fasta file manipulation

6 minute read

Published:

This bit of code can be a great help to subset a Fasta file alignment based on certain conditions taken from a sample information file (e.g. subset only the samples collected in Spring, or those in Winter and greater than y cm, or everything except those in Autumn, etc.).

Plot a phylogeny in R using ggtree

2 minute read

Published:

This post will show you how to generate a phylogeny plot in R, with a heatmap alongside it. This example uses binary data, but it can be adapted to be plotted with a continuous variable.

Creating a climate map with GPS coordinate points

3 minute read

Published:

This R code shows you how to plot a map for a desired country or geographic region, and how to display a chosen climatic variable (e.g. mean annual temperature, annual precipitation) as an overlay. The WorldClim dataset has 19 variables to choose from.

Renaming all the sequences in a FASTA file automatically

2 minute read

Published:

I came across the problem of renaming sequences in a FASTA sequence alignment after downloading over 200 sequences from GenBank for four different genes. The sequence names were assigned by the GenBank accession number (e.g. MK1526) only. I wanted the sequence names to have the species name in it as well, for example MK1526_Canis_lupis. To avoid the tedious task of manually doing this, I wrote a few lines of R code that I hope will be of use to others with the same issue.