Plot different colours based on the conditions - r

Question

This is the first 10 rows of my data frame:
head(test.data,10)
# A tibble: 10 x 5
date o2.permeg co2.ppm apo o2.spike
<time> <dbl> <dbl> <dbl> <chr>
1 2015-01-01 00:00:00 -685.09 413.023 -354.1816 N
2 2015-01-01 00:02:00 -695.10 412.894 -364.8690 N
3 2015-01-01 00:04:00 -687.84 412.979 -357.1627 N
4 2015-01-01 00:06:00 -683.23 412.866 -353.1460 N
5 2015-01-01 00:08:00 -683.28 412.755 -353.7788 N
6 2015-01-01 00:10:00 -685.40 412.647 -356.4659 N
7 2015-01-01 00:12:00 -687.80 412.659 -358.8029 N
8 2015-01-01 00:14:00 -662.79 412.665 NA Y
9 2015-01-01 00:16:00 -684.17 412.762 -354.6321 N
10 2015-01-01 00:18:00 -680.37 412.720 -351.0526 N
As you can see there's a last column named o2.spike, which has characters N and Y in it. N means that the data point is not a spike, and Y means that it is a spike. In this sample, there's only 1 Y, but in the real frame, there are loads, and randomly placed.
My desire is to plot all the data points in a plot, and those marked with Y will be plotted in a different colour.
For your information, this is the current code that I am using to plot everything. The first 3 variables are plotted in red, green, and blue, and I want the "Y" rows to be plotted in as, for example, pink.
library(openair)
test.data$yr_day <- format(as.Date(test.data$date), "%Y-%m-%d")
dir.create(daily) # where "daily" is the path of the folder I want to save the plots into
for (d in unique(test.data$yr_day)) {
mypath <- file.path(daily, paste(name, d, ".png", sep = "" ))
png(filename = mypath, width = 963, height = 690)
timePlot(subset(test.data, yr_day == d),
plot.type = "p",
pollutant = c("co2.ppm", "o2.permeg", "apo"),
y.relation = "free",
date.pad = TRUE,
pch = c(19,19,19),
cex = 0.2,
xlab = paste("Time of day in hours on", d),
ylab = "CO2, O2, and APO concentrations",
name.pol = c("CO2 (ppm)", "O2 (per meg)", "APO (per meg)"),
date.breaks = 24,
date.format = "%H:%M"
)
dev.off()
}
An example plot (containing all the spikes with the same colour as the non-spike ones) is as follows:
So how do I plot the spikes in a different colour from the others? Thank you very much!
Edit:
As asked by Sebastian, I have added this (not sure how you guys will be able to extract the data from that)
dput(head(test.data,20))
structure(list(date = structure(c(1420070400, 1420070520, 1420070640,
1420070760, 1420070880, 1420071000, 1420071120, 1420071240, 1420071360,
1420071480, 1420071600, 1420071720, 1420071840, 1420071960, 1420072080,
1420072200, 1420072320, 1420072440, 1420072560, 1420072680), class = c("POSIXct",
"POSIXt"), tzone = "GMT"), o2.permeg = c(-685.09, -695.1, -687.84,
-683.23, -683.28, -685.4, -687.8, -662.79, -684.17, -680.37,
-684.66, -686.13, -683.27, -680.77, -682.16, -692.54, NA, NA,
NA, NA), co2.ppm = c(413.023, 412.894, 412.979, 412.866, 412.755,
412.647, 412.659, 412.665, 412.762, 412.72, 412.692, 412.71,
412.757, 412.838, 412.922, 413.019, NA, NA, NA, NA), apo = c(-354.181646778043,
-364.868973747017, -357.162673031026, -353.145990453461, -353.778806682578,
-356.465871121718, -358.802863961814, NA, -354.632052505966,
-351.052577565632, -355.489594272076, -356.86508353222, -353.75830548926,
-350.833007159904, -351.781957040573, -361.652649164678, NA,
NA, NA, NA), o2.spike = c("N", "N", "N", "N", "N", "N", "N",
"Y", "N", "N", "N", "N", "N", "N", "N", "N", "N", "N", "N", "N"
)), .Names = c("date", "o2.permeg", "co2.ppm", "apo", "o2.spike"
), row.names = c(NA, -20L), class = c("tbl_df", "tbl", "data.frame"
))

Answer 1

Unfortunately, without having data, it's not easy to answer the question.
A ggplot2 solution could be:
g1 <- ggplot(data=test.data, aes(x=date, y=o2.permeg, col=o2.spike)) + geom_point()
g1
Passing a column of the dataframe to parameter "col" in "aes" makes you map with different colors every different value in that column.
It creates even a legend, with names associated to different colors.
I tried this with another dataframe ("iris", contained in base R) and it worked, hope it will be helpful.
Edit:
To have side-by-side plots, you can create 3 plots with ggplot and the use the function plot_grid() provided by "cowplot" package.
library(cowplot)
g1 <- ggplot(data=test.data, aes(x=date, y=o2.permeg, col=o2.spike)) + geom_point()
g2 <- ggplot(data=test.data, aes(x=date, y=co2.ppm, col=o2.spike)) + geom_point()
g3 <- ggplot(data=test.data, aes(x=date, y=apo, col=o2.spike)) + geom_point()
plot_grid(g1, g2, g3, nrow=3, ncol=1)