amp_heatmap drops the first "s" in a species name

[hmaru]

Hi,

When I make a heatmap with amp_heatmap(), it seems to always drop the first letter "s" in a species name. For example, "(Nitrospira) sublineage I" becomes "ublineage I". The above example occurred with the minimal example data indicated in the turorial.

Other examples seen with my own data include,

• "(Neisseria) subflava" changed to "ubflava"
• "(Alloprevotella) sp._HMT_914" changed to "p._HMT_914" etc What I noticed so far is only the first "s" in species names, but not sure if that's all.

I tried to make a reproducible example with reprex, but couldn't figure out how to make it with read.csv() reading local files, so I just copy my script below. Here I'm just reading the minimal example csv files downloaded to my computer.

library(ampvis2)

myotutable <- read.csv("example_otutable.csv", check.names = FALSE)
mymetadata <- read.csv("example_metadata.csv", check.names = FALSE)

d <- amp_load(otutable = myotutable,
              metadata = mymetadata)

amp_heatmap(d, 
            tax_aggregate = "Species",
            tax_add = "Genus", 
            tax_empty = "OTU", 
            )

This is the output image, with a missing "s".

---

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134) Matrix products: default locale: [1] LC_COLLATE=Japanese_Japan.932 LC_CTYPE=Japanese_Japan.932
[3] LC_MONETARY=Japanese_Japan.932 LC_NUMERIC=C
[5] LC_TIME=Japanese_Japan.932
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] ampvis2_2.6.4 ggplot2_3.3.2

[KasperSkytte]

Hi there

That is a bug. A bad regular expression, you have to reinstall.

library(ampvis2)
#> Loading required package: ggplot2

d <- amp_load(otutable = example_otutable,
              metadata = example_metadata)

amp_heatmap(d,
            tax_aggregate = "Species",
            tax_add = "Genus",
            tax_empty = "OTU",
)
#> Warning: Transformation introduced infinite values in discrete y-axis

^{Created on 2020-09-01 by the reprex package (v0.3.0)}

[hmaru]

Thanks a lot for the quick update! I get the desired output and it saved me a lot of time to make the figures!