R novice and trying to improve the appearance of grouped box plots - r

Question

I found some online datasets and managed to make some complex box plots that had most of the features I was looking for. I'd appreciate the community's help in making these plots look better, such as:
removing axes lines,
adding tick marks and making them point inwards,
changing the background color or font of facet_wrap,
and removing "Label" in my attached plots.
The program Veusz allows you to change whisker mode to (e.g. I.5 IQR, 9/91 percentile, 1 stddev) and it would be nice to have that option as well. I also don't understand why the data points in my first box plot (linked below) are off center.
Linked below are screen shots of some grouped box plots that I made from my own data. I learn best by breaking and fixing things, and if someone has the time to write out the code for a box plot with lots of features, I will deconstruct it to see what each part does and search for the code online to get a better understanding of how it works.
Box plot of my data 1
Box plot of my data 2
Box plot of my data 3
structure(list(X. = structure(c(1L, 12L, 23L, 34L, 45L, 56L,
67L, 71L, 72L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 13L,
14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 24L, 25L, 26L, 27L,
28L, 29L, 30L, 31L, 32L, 33L, 35L, 36L, 37L, 38L, 39L, 40L, 41L,
42L, 43L, 44L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L,
57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 68L, 69L, 70L
), .Label = c("# 1", "# 10", "# 11", "# 12", "# 13", "# 14",
"# 15", "# 16", "# 17", "# 18", "# 19", "# 2", "# 20", "# 21",
"# 22", "# 23", "# 24", "# 25", "# 26", "# 27", "# 28", "# 29",
"# 3", "# 30", "# 31", "# 32", "# 33", "# 34", "# 35", "# 36",
"# 37", "# 38", "# 39", "# 4", "# 40", "# 41", "# 42", "# 43",
"# 44", "# 45", "# 46", "# 47", "# 48", "# 49", "# 5", "# 50",
"# 51", "# 52", "# 53", "# 54", "# 55", "# 56", "# 57", "# 58",
"# 59", "# 6", "# 60", "# 61", "# 62", "# 63", "# 64", "# 65",
"# 66", "# 67", "# 68", "# 69", "# 7", "# 70", "# 71", "# 72",
"# 8", "# 9"), class = "factor"), Label = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L), .Label = c("Sample 1", "Sample 2", "Sample 3"
), class = "factor"), Rescan = structure(c(1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L,
4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L,
3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L,
4L, 4L, 4L), .Label = c("Rescan 0", "Rescan 1", "Rescan 2", "Rescan 3"
), class = "factor"), Porosity = c(15.19, 15.72, 15.83, 15.57,
15.11, 14.15, 17.24, 17.53, 18.21, 18.8, 18.32, 19.59, 17.4,
17.98, 19.33, 18.94, 18.32, 18.17, 19.67, 20.55, 19.04, 18.18,
19.59, 18.19, 18.97, 18.64, 18.83, 17.24, 18.09, 17.74, 22.28,
22.29, 21.35, 21.96, 23.12, 22.9, 22.9, 21.06, 23.34, 22.82,
21.42, 20.48, 21.22, 22.75, 21.62, 22.24, 24.28, 20.48, 14.79,
13.69, 13.4, 14.46, 14.13, 13.55, 20.67, 19.81, 21.2, 20.77,
22.29, 21.94, 19.49, 19.29, 19.43, 20.31, 21.77, 19.39, 22.37,
21.46, 21.86, 21.58, 21.82, 23.02)), class = "data.frame", row.names = c(NA,
-72L))

Answer 1

Here's an example of your plot with the things you wanted to do. I suppose you can adjust the code to your needs from here:
ggplot(mydata, aes(Label,Porosity,fill=Label))+
geom_boxplot()+
# shift strips down
facet_wrap(~Rescan, strip.position = "bottom")+
# add exact points
geom_point(alpha=0.2)+
# add your preferred colors here (hexcode also works fine)
scale_fill_manual(values=c("red","blue","green"))+
# appearance
theme_classic()+
# legend options
theme(legend.title = element_blank(),
legend.text = element_text(color ="black", size = 8),
legend.position = "top", # "bottom" or "right"
legend.key.size = unit(1, "cm"),
legend.spacing.x = unit(5, "mm"),
legend.direction = "horizontal", # or "vertical"
legend.background = element_blank())+
# reverse legend keys
guides(fill = guide_legend(reverse = F))+ # set T to take action
# scaling y-axis
scale_y_continuous(expand = c(0, 0), limits = c(0,max(mydata$Porosity)),breaks = seq(0,max(mydata$Porosity,10)))+
# paramaters of the axes
theme(
axis.text = element_text(color = "black", angle = 0, hjust = 0.5, vjust = 0.5, size = 8),
# axis.title = element_blank(), # activate for no axis titles
axis.line = element_line(color = "black", size = 0.5), # use element_blank() for no lines
axis.ticks.length=unit(-0.1, "cm"), # negative values turn them inside
plot.background = element_blank(),
text = element_text(family = "Arial"),
strip.background = element_blank(),
strip.placement = "outside")+ # or "inside"
# name your axes
ylab("your y lab")+
xlab("your x lab")+
# add x-axis in each facet
annotate("segment", y=0,yend=0,x=0,xend=Inf)

Answer 2

Hopefulyy this answers some of the questions, but to be honest it's hard to pull out the individual questions you are asking. Perhaps put them in dot points?
overall look:
There are some pre-made themes you can try, I like:
theme_void() - removes most things
theme_classic() - makes the background nicer to look at
theme_minimal() - removes the outer border and makes the background prettier
You can add them as a layer with + theme_void() on the end of the plotting code.
For all other specific customisations look at ?theme() as there are a whole bunch of things you can do.
labels:
To remove the title 'label' add labs(legend = '') as a layer. You can also use this to modify the x, y, caption and title text.
If you want to remove the legend entirely, you can add show.legend = F inside your geom_jitter() layer. (e.g. geom_jitter(show.legend = F)) This will mean it shows on the graph, but nothing appears in the legend.
facets:
To change the colour of the background in facte_wrap use theme(strip.background = element_rect(color = 'desired_colour'))
To change the colour of the text in facte_wrap use theme(strip.text = element_text(color = 'desired_colour'))
axis lines:
add theme(axis.line = element_blank())
points:
Your points are off center due to the geom_jitter(). Try geom_point() instead.