Issues in fig2.R (identified in SIB days reproducibility hackathon)

[ikeller]

1. Class checks in seqLogo2 not working:

`seqLogo2(pwm,xfontsize=6, yfontsize=6, title="Class 1 (Inr+DPE), 37.2%")
Error in if (class(pwm) == "pwm") { : the condition has length > 1

class(pwm)
[1] "matrix" "array"`

As a work around: comment out lines 3-13 in seqLogo2_fig2.R

2. Wrong input files linked for human plot

[ikeller]

sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Europe/Zurich
tzcode source: internal

attached base packages:
[1] grid stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0