Make a PCA plot in Bash with the OpenCPU API

out.pdf

pca.sh

#!/usr/bin/env bash
# pca.sh
#
# Kamil Slowikowski
# 2019-02-04
#
# Make a PCA scatter plot in Bash
# ===============================
#
# This script uses curl to make HTTP requests to call R functions on a remote
# server. Since it is a public server running OpenCPU, anyone can call
# functions on it.
#
# Check out OpenCPU
# -----------------
#
#   https://www.opencpu.org/api.html
#

# Show Bash commands as they are executed.
# set -x

# Example 1
#
# Get 3 numbers from a normal distribution with mean = 10 and sd = 10
#
#   curl http://cloud.opencpu.org/ocpu/library/stats/R/rnorm/json \
#   -H "Content-Type: application/json" -d '{"n":3, "mean": 10, "sd":10}'

# Example 2
#
# Run prcomp on a local matrix in a compressed TSV file.

content="S1	S10	S100	S101	S103
87.4781	72.6434	113.892	98.765	90.5169
64.2295	98.6086	102.7	76.0872	74.7082
1.55164	1.82674	1.31479	1.08724	2.63889
12.8908	28.9163	50.4726	35.169	13.6802
3.68155	1.14048	0	0.417137	0.386618
"

file="mat.tsv.gz"

echo "$content" | gzip > "$file"

# Check that the contents are written properly.
# gzip -cd $file

OCPU=http://cloud.opencpu.org/ocpu

function ocpu() {
  command curl -s $OCPU/$1 $2 $3 | head -n1 | cut -f4 -d/
}

x=$(ocpu library/readr/R/read_tsv -F "file=@${file}")
x=$(ocpu library/stats/R/prcomp -d "x=${x}")
x=$(ocpu library/graphics/R/plot -d 'x='${x}'::.val$x[,1:2]')

curl -s $OCPU/tmp/$x/graphics/last/pdf?width=8 > out.pdf