Log scale in R help :)

[drlawson]

Hi all, I made this figure and table to represent metadata from the nightingales datasheet. I want the y axis to be logarithmic so you can actually see the values for each primary taxa. However, when i add the log scale on the y axis, the data seems to be incorrect (shows P_generosa as having more than O_lurida which is not correct). Anyone know how to solve this? Or am I interpreting this incorrectly? Thanks :)

My code for the table is

data(nightingales)
nighttable <- (nightingales %>% group_by(Primary_taxa, Molecule) %>% summarize(n = n(), .groups = "keep"))
options(knitr.kable.NA = '0')
nighttable %>% pivot_wider(names_from = Molecule, values_from = n) %>% kbl(digits=2) %>% kable_classic(full_width = F, html_font = "Cambria")

My code for the first figure is

cols <- c("DNA" = "darkblue", "RNA" = "cornflowerblue", "Unknown" = "darkgray")
ggplot(data = nighttable, aes(x = Primary_taxa, y = n, fill = Molecule)) + geom_bar(position= "stack", stat="identity") +
scale_x_discrete(guide = guide_axis(angle = -90)) + theme_classic() + scale_fill_manual(values = cols)

My code for the second figure is

cols <- c("DNA" = "darkblue", "RNA" = "cornflowerblue", "Unknown" = "darkgray")
ggplot(data = nighttable, aes(x = Primary_taxa, y = n, fill = Molecule)) + geom_bar(position= "stack", stat="identity") +
scale_x_discrete(guide = guide_axis(angle = -90)) + theme_classic() + scale_fill_manual(values = cols) + scale_y_log10()

[laurahspencer]

Have you tried to transform n in your figure, like this- y = log(n)

…

On Fri, Oct 8, 2021 at 6:13 PM Delaney Lawson ***@***.***> wrote: Hi all, I made this figure and table to represent metadata from the nightingales datasheet. I want the y axis to be logarithmic so you can actually see the values for each primary taxa. However, when i add the log scale on the y axis, the data seems to be incorrect (shows P_generosa as having more than O_lurida which is not correct). Anyone know how to solve this? Or am I interpreting this incorrectly? Thanks :) My code for the table is data(nightingales) nighttable <- (nightingales %>% group_by(Primary_taxa, Molecule) %>% summarize(n = n(), .groups = "keep")) options(knitr.kable.NA = '0') nighttable %>% pivot_wider(names_from = Molecule, values_from = n) %>% kbl(digits=2) %>% kable_classic(full_width = F, html_font = "Cambria") My code for the first figure is cols <- c("DNA" = "darkblue", "RNA" = "cornflowerblue", "Unknown" = "darkgray") ggplot(data = nighttable, aes(x = Primary_taxa, y = n, fill = Molecule)) + geom_bar(position= "stack", stat="identity") + scale_x_discrete(guide = guide_axis(angle = -90)) + theme_classic() + scale_fill_manual(values = cols) My code for the second figure is cols <- c("DNA" = "darkblue", "RNA" = "cornflowerblue", "Unknown" = "darkgray") ggplot(data = nighttable, aes(x = Primary_taxa, y = n, fill = Molecule)) + geom_bar(position= "stack", stat="identity") + scale_x_discrete(guide = guide_axis(angle = -90)) + theme_classic() + scale_fill_manual(values = cols) + scale_y_log10() [image: Screen Shot 2021-10-08 at 4 05 20 PM] <https://user-images.githubusercontent.com/73162507/136633193-e8c67d1c-e3e5-49f6-87cd-dfdf97872ce3.png> [image: Screen Shot 2021-10-08 at 4 05 42 PM] <https://user-images.githubusercontent.com/73162507/136633217-a4ba2bfb-aab7-45f1-90c0-59dc82fe9a60.png> [image: Screen Shot 2021-10-08 at 4 05 53 PM] <https://user-images.githubusercontent.com/73162507/136633227-1b872d2b-28aa-4b43-8033-47435c692b55.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1312>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEDXA7JXVNJ25YCE26CUFMTUF53G5ANCNFSM5FUR3S7Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[drlawson]

Thanks for the suggestion Laura! I actually wanted to transform just the y axis instead of the data. I ended up needing to switch to using plotly instead of ggplot but I finally got it!! :)