Region plot 'a' in the legend plot

[karpat90]

Hello!

Thank you for a great package!

When I am using region_plot(), if the second dataset has no genome-wide significant hits, a red 'a' appears in the plot legend.

Could you help me with this

Thank you

[totajuliusd]

Hello,

Can you please show me the command you are using and maybe a screenshot of the plot? I tried to reproduce this using the test data, but everything looks ok when I do:

regionplot(list(CD_UKBB, UC_UKBB %>% dplyr::filter(P>1e-5)), gene="IL23R")

Tota

[karpat90]

I have used this command

regionplot(list(df2,df), region="chr6:106053916-107309327", sign_thresh = 0.01, annotate_with_vline = 5e-03, build = 37, legend_labels = c("ph1", "ph2"), protein_coding_only = TRUE, legend_text_size = 15, axis_text_size = 15, axis_title_size = 15, label_size = 4)

[totajuliusd]

Hmmm... that is odd, and something I havent seen before.

What happens if you do:

regionplot(list(df2%>% select(CHROM,POS,P) %>% na.omit(),df %>% select(CHROM,POS,P) %>% na.omit()), region="chr6:106053916-107309327",
         sign_thresh = 0.01,
         annotate_with_vline = 5e-03, build = 37,
         legend_labels = c("ph1", "ph2"),
          protein_coding_only = TRUE,legend_text_size = 15, axis_text_size = 15, axis_title_size = 15, label_size = 4)

[karpat90]

It's still produces the same figure with 'a'

[totajuliusd]

What happens if you replace your dataframes with the test data?

regionplot(list(CD_UKBB,CD_FINNGEN), region="chr6:106053916-107309327",
         sign_thresh = 0.01,
         annotate_with_vline = 5e-03, build = 37,
         legend_labels = c("ph1", "ph2"),
          protein_coding_only = TRUE,legend_text_size = 15, axis_text_size = 15, axis_title_size = 15, label_size = 4)

And which version of topr are you using?

[karpat90]

When I use the command you have suggested I also get plot with NA

[totajuliusd]

Which version of topr are you using? You can use sessionInfo()or ?toprto see the version.

[karpat90]

I am using topr_2.0.0

[totajuliusd]

Which version of ggplot2 are you using? It looks fine for me and Im using ggplot2_3.4.4. Can you show me the output from the sessionInfo() command?

[karpat90]

I am using ggplot2_3.5.0, the latest one

[totajuliusd]

That is strange - wich operating system are you on?

[karpat90]

I ma using Mac

[totajuliusd]

I get the same error after upgrading ggplot2 to version 3.5.0. So this is an error that comes with using the most recent version of ggplot2 with topr, and something I need to fix asap.

Until then, you can use topr with an older ggplot version, by doing for example:

install.packages(" http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.4.4.tar.gz", repos=NULL, type="source")

Thank you for bringing this to my attention!

[karpat90]

Unfortunately, when I use ggplot2 version you have suggested, I get 'a' strings elsewhere:

[totajuliusd]

Can you move the legend tvo the right by adding this argument:

legend_position=“right”

Im not sure what is causing this and going to have to look into this properly, but wont have time to do it until later this week.

[totajuliusd]

Hi again, The code causing the problem has been identified and fixed in topr v2.0.1 which will be submitted to CRAN today, so it should become publicly available within the next few days!

[totajuliusd]

topr v2.0.1 is now available on CRAN and downloadable via install.packages