R help - Jul 2023 - how to change the y-axis to logarithmic in a barplot ggplot

Dear all,?


I am having the following dataset
fc<-
ID? ? values? ? databases
Al? ? 0.15? ? phreeqc
Al? ? 0.6? ? carbfix
Al? ? 0.47? ? actual
Ca? ? 7.2? ? phreeqc
Ca? ? 7.2? ? carbfix
Ca? ? 0.3? ? actual
Na? ? 14.4? ? phreeqc
Na? ? 84? ? carbfix
Na? ? 106? ? actual
Cl? ? 22? ? phreeqc
Cl? ? 21.9? ? carbfix
Cl? ? 72.1? ? actual
Fe? ? 0.05? ? phreeqc
Fe? ? 0.43? ? carbfix
Fe? ? 1.25? ? actual
Mg? ? 0.35? ? phreeqc
Mg? ? 0.17? ? carbfix
Mg? ? 0.08? ? actual
SO4? ? 0? ? phreeqc
SO4? ? 0? ? carbfix
SO4? ? 416? ? actual


As you can see, the values range from 0 to 400. I want it to plot it in bars;
when I am plotting it as you can imagine the values near zero don't show at
all. So I am trying to make the y axis logarithmic. I have created the following
code but it doesn't work. I get the bars with zero above and the others on
top.?


ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +?
geom_bar(stat = "identity", position = "dodge",
aes(y=log(mean)))?
+ theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title =
element_blank())?
+ scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette =
"Dark2")


I would very much appreciate your help. I am stuck.?


Kind regards,
Maria

On 7/16/23 14:51, Maria Lathouri via R-help wrote:
> Dear all,
>
>
> I am having the following dataset
> fc<-
> ID? ? values? ? databases
> Al? ? 0.15? ? phreeqc
> Al? ? 0.6? ? carbfix
> Al? ? 0.47? ? actual
> Ca? ? 7.2? ? phreeqc
> Ca? ? 7.2? ? carbfix
> Ca? ? 0.3? ? actual
> Na? ? 14.4? ? phreeqc
> Na? ? 84? ? carbfix
> Na? ? 106? ? actual
> Cl? ? 22? ? phreeqc
> Cl? ? 21.9? ? carbfix
> Cl? ? 72.1? ? actual
> Fe? ? 0.05? ? phreeqc
> Fe? ? 0.43? ? carbfix
> Fe? ? 1.25? ? actual
> Mg? ? 0.35? ? phreeqc
> Mg? ? 0.17? ? carbfix
> Mg? ? 0.08? ? actual
> SO4? ? 0? ? phreeqc
> SO4? ? 0? ? carbfix
> SO4? ? 416? ? actual
>
>
> As you can see, the values range from 0 to 400. I want it to plot it in
bars; when I am plotting it as you can imagine the values near zero don't
show at all. So I am trying to make the y axis logarithmic. I have created the
following code but it doesn't work. I get the bars with zero above and the
others on top.
>
>
> ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +

None of those aes() names are in your data object. They should be one of

ID? ? values? ? databases

> geom_bar(stat = "identity", position = "dodge",
aes(y=log(mean)))
What are you intending with `

aes(y=log(mean)

`
> + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor =
element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title =
element_blank())
> + scale_fill_brewer(palette = "Dark2") +
scale_color_brewer(palette = "Dark2")
-- 

David.
>
> I would very much appreciate your help. I am stuck.
>
>
> Kind regards,
> Maria
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Try adding

scale_y_log10()

This is a general R help list. It's not a ggplot list and you are likely to
be chased off to ggplot's package maintainers nominated support pages.

But really a Google search should surely have found this?



On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help, <r-help at
r-project.org>
wrote:
> Dear all,
>
> ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +
> geom_bar(stat = "identity", position = "dodge",
aes(y=log(mean)))
> + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor
> = element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title
> element_blank())
> + scale_fill_brewer(palette = "Dark2") +
scale_color_brewer(palette > "Dark2") +
>
scale_y_log10()

	[[alternative HTML version deleted]]

On Sun, 16 Jul 2023 21:51:10 +0000 (UTC)
Maria Lathouri via R-help <r-help at r-project.org> wrote:
> As you can see, the values range from 0 to 400. I want it to plot it
> in bars; when I am plotting it as you can imagine the values near
> zero don't show at all.
A logarithmic scale won't work when the range of numbers to display
includes 0. It would have worked if it was some small non-zero
quantity, but an actual zero is infinitely far down; it won't fit.

There is a number of transformations described in
help(scale_y_continuous). You may find trans="pseudo_log" or
trans="sqrt" useful.

help(geom_bar) recommends geom_col() instead of geom_bar() to represent
values (not counts of occurrences).

We could help you more efficiently if you clarified the relationship
between your data (with columns `ID`, `values`, `databases`) and your
code (which mentions `Temp`, `mean`, `Glass`).

-- 
Best regards,
Ivan