V5

Question 1

how to define your own simple object with class

Answer 1

#first define the object - needs to be list
my object  add your own new class
class(myobject)

Question 2

how to code a custom print

Answer 2

print.myclass

Question 3

how to overload a plot (code)

Answer 3

when error “do not know how to / cannot coerce” pops up

- plot.myclass

Question 4

whats the difference when you overload an image instead of a plot

Answer 4

• doesn’t work on list, only matrix

Question 5

whats the plotting philosophy and why is it good/bad?

Answer 5

“Artist’s palette” model

• start with blank canvas and build up from there
• start with plot function (or similar)
• use annotation functions to add/modify (text, lines, points, axis)

• convenient, mirrors how we think of building plots and analysing data
• can’t go back once plot has started (i.e. to adjust margins); need to plan in advance
• difficult to “translate to others once a new plot has been created(no graphical “language”)
• Plot is just a series of R commands

Question 6

important plotting parameters

Answer 6

pch - plotting symbol
lty - line type
lwd - line width
col - plotting color
xlab - character string for the x-axis label
ylab - character string for the y-axis label

Question 7

what is the par() function

Answer 7

used to specify global graphics parameters that affect all plots in an R session. These parameters can be overridden when specified as arguments to specific plotting functions

Question 8

important parameters of the par() function

Answer 8

las - orientation of the axis labels on the plot
bg - the background colour
mar - margin size
oma - outer margin size
mfrow - number of plots per row, column (plots are filled row-wise)
mccollum - number of plots period, column (plots are filled column wise)

Question 9

how to get current par settings of colour (example)

Answer 9

par(“col”)

[1] “black”

Question 10

functions that are vital for plotting (7)

Answer 10

plot - make a scatterplot, or other type of plot depending on the class of the object being plotted
lines - add lines to a plot, given a vector x values and a corresponding vector of y values (or a 2-column matrix); this function just connects the dots)
points - add points to a plot
text - add text labels to a plot using specified x, y coordinates
title - add annotations to x, y axis labels, title, subtitle, outer margin (plots outside of plot window)
mtext - add arbitrary text to the margins (inner or outer) of the plot
axis - adding axis tracks / labels

Question 11

colour and ranges

Answer 11

for example: rainbow , heat.colors, etc

gray()

Question 12

how to code transparency

Answer 12

rgb(red, green, blue, alpha) -> alpha = 1 max visible , alpha = 0 minimum visible

Question 13

the with() function

Answer 13

• because plots can become bulky
• convenience function
• turns columns of data.frames into variables
• this is why read.table has check.names

mydata[,”Ozone”]
with(my data,{
mean(Ozone)
})

-> to get the mean of the column

Question 14

how to build up a plot (code)
# plot all wind zone per ozone in Ny with header title

highlight within plot month 5 data in blue and all other read

add legend

Answer 14

plot all wind zone per ozone in Ny with header title
with(air quality,
plot(Wind, Ozone,
main = “Ozone and Wind in NY”))

highlight within plot month 5 data in blue and other blue

with(subset(air quality, Month == 5),
points(Wind, Ozone, col = “blue”))

with(subset(air quality, Month != 5),
points(Wind, Ozone, col = “red”))

add legend

legend(“topright”, pch = 1, col = c(“blue”, “red”), legend = c(“May”, “Other Months”))

Question 15

how to add a best fit line (code)

Answer 15

# y = a + bx
model

Question 16

how to make multiple base plots

Answer 16

• only if variable names are valid

- par (mfrow = c(1,3), oma = c(0,0,2,0)){
#all the plots you are gonna code
}

oma for space between plots

Question 17

how to code a pie chart with percentages

Answer 17

slices

Question 18

hot to code a dendrogram

• labels at same level

Answer 18

# prepare hierarchical closer
hc = hclust(dist(mtcars))
-> dist to calculate distance, hclust to cluster those distances

#very simple dendrogram
plot(hc)

# labels at the same level
plot(hc, hand = -1)

Question 19

how to plot a dendrogram in more ways

Answer 19

# create a dendrogram object
hcd = as.dendrogram(hc)

Question 20

four different phylogenic trees + library

how to code

Answer 20

library(ape)

#plot basic tree
plot(as.phylo(hc), cex = 0.9, label.offset = 1)

# cladogram
plot(as.phylo(hc), type = "cladogram", cex = 0.9, label.offset = 1)

# unrooted
plot(as.phylo(hc), type = "unrooted")

#fan
plot(as.phylo(hc), type = "fan"