Misc. data viz
Last updated: 2021-07-03
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Knit directory: wildlife-haemoprotozoa/
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| Rmd | d429fdd | siobhon-egan | 2021-03-18 | First publish |
This page to host some misc. data visualization and notes for phylogenetics.
Haemoprotozoa prevalence
Import data
library(readr)
haem <- read_csv("data/haemoprotozoa.csv")
── Column specification ────────────────────────────────────────────────────────
cols(
gDNA_ID = col_character(),
species_code = col_character(),
`Hepatozoon sp.` = col_double(),
`Babesia lohae-like` = col_double(),
`Theileria cf. peramelis` = col_double(),
`Trypanosoma lewisi-like` = col_double(),
`Trypanosoma noyesi` = col_double(),
`Trypanosoma gilletti` = col_double(),
`Trypanosoma cyclops-like` = col_double()
)UpSetR plot
Creating UpSetR and the add on ComplexUpset plot to show co-infections, Extra examples here
Load libraries
Load data
Must be in a dataframe format
# convert to dataframe
haemdf <- as.data.frame(haem)
str(haemdf)'data.frame': 134 obs. of 9 variables:
$ gDNA_ID : chr "QUE001-M" "CHU001-QIA" "CHU002-M" "CHU003-M" ...
$ species_code : chr "Quenda" "Chuditch" "Chuditch" "Chuditch" ...
$ Hepatozoon sp. : num 0 0 0 0 0 0 0 0 0 0 ...
$ Babesia lohae-like : num 0 0 0 0 0 0 0 0 1 1 ...
$ Theileria cf. peramelis : num 0 0 0 0 0 0 0 0 0 0 ...
$ Trypanosoma lewisi-like : num 0 0 0 0 0 0 0 0 0 0 ...
$ Trypanosoma noyesi : num 0 0 0 0 0 0 0 0 0 0 ...
$ Trypanosoma gilletti : num 0 0 0 0 0 0 0 0 0 0 ...
$ Trypanosoma cyclops-like: num 0 0 0 0 0 0 1 1 0 0 ...
- attr(*, "spec")=
.. cols(
.. gDNA_ID = col_character(),
.. species_code = col_character(),
.. `Hepatozoon sp.` = col_double(),
.. `Babesia lohae-like` = col_double(),
.. `Theileria cf. peramelis` = col_double(),
.. `Trypanosoma lewisi-like` = col_double(),
.. `Trypanosoma noyesi` = col_double(),
.. `Trypanosoma gilletti` = col_double(),
.. `Trypanosoma cyclops-like` = col_double()
.. )# define columns with species info
haem_sp = colnames(haemdf)[3:9]
haem_sp[1] "Hepatozoon sp." "Babesia lohae-like"
[3] "Theileria cf. peramelis" "Trypanosoma lewisi-like"
[5] "Trypanosoma noyesi" "Trypanosoma gilletti"
[7] "Trypanosoma cyclops-like"Simple UpSetR plot
upsetR1 = upset(haemdf, sets = c("Hepatozoon sp.", "Babesia lohae-like", "Theileria cf. peramelis", "Trypanosoma lewisi-like", "Trypanosoma noyesi", "Trypanosoma gilletti", "Trypanosoma cyclops-like"), sets.bar.color = "#7a255d")
upsetR1
| Version | Author | Date |
|---|---|---|
| 2d0d4fb | siobhon-egan | 2021-07-02 |
More detailed plots using ComplexUpset
library(ComplexUpset)
Attaching package: 'ComplexUpset'The following object is masked from 'package:UpSetR':
upsetupsetR3 = upset(
haemdf,
haem_sp, width_ratio=0.1,
base_annotations=list(
'Intersection size'=intersection_size(
counts=TRUE,
mapping=aes(fill=species_code)
))
)
upsetR3
| Version | Author | Date |
|---|---|---|
| 2d0d4fb | siobhon-egan | 2021-07-02 |
upsetR4 = upset(
haemdf, haem_sp,
set_sizes=(
upset_set_size(
geom=geom_bar(
aes(fill=species_code, x=group)
),
position='right'
)
),
# moves legends over the set sizes
guides='over'
)
upsetR4
| Version | Author | Date |
|---|---|---|
| 2d0d4fb | siobhon-egan | 2021-07-02 |
Phylogenetics
All phylogenetics created in related manuscript was done using IQTEE.
My detailed notes on using IQTREE server for generated phylogenies is here.
Trees visualised using FigTree and annotated in inkscape.
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ComplexUpset_1.1.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5
[5] purrr_0.3.4 tidyr_1.1.2 tibble_3.1.0 ggplot2_3.3.3
[9] tidyverse_1.3.0 UpSetR_1.4.0 readr_1.4.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lubridate_1.7.10 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.27 utf8_1.2.1 R6_2.5.0 cellranger_1.1.0
[9] plyr_1.8.6 backports_1.2.1 reprex_1.0.0 evaluate_0.14
[13] highr_0.8 httr_1.4.2 pillar_1.5.1 rlang_0.4.10
[17] readxl_1.3.1 rstudioapi_0.13 whisker_0.4 jquerylib_0.1.3
[21] rmarkdown_2.7.2 labeling_0.4.2 munsell_0.5.0 broom_0.7.5
[25] compiler_4.0.3 httpuv_1.5.5 modelr_0.1.8 xfun_0.21
[29] pkgconfig_2.0.3 htmltools_0.5.1.1 tidyselect_1.1.0 gridExtra_2.3
[33] fansi_0.4.2 crayon_1.4.1 dbplyr_2.1.0 withr_2.4.1
[37] later_1.1.0.1 grid_4.0.3 jsonlite_1.7.2 gtable_0.3.0
[41] lifecycle_1.0.0 DBI_1.1.1 git2r_0.28.0 magrittr_2.0.1
[45] scales_1.1.1 cli_2.3.1 stringi_1.5.3 farver_2.0.3
[49] fs_1.5.0 promises_1.2.0.1 xml2_1.3.2 bslib_0.2.4.9001
[53] ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.7 tools_4.0.3
[57] glue_1.4.2 hms_1.0.0 yaml_2.2.1 colorspace_2.0-0
[61] rvest_0.3.6 knitr_1.31 haven_2.3.1 patchwork_1.1.1
[65] sass_0.3.1 Project website by Siobhon L. Egan, 2021. This site was created in R Markdown with workflowr