Modifies dot plots to have different sizes of dots mimicking violin plots and identifies modes or peaks for them (Rosenblatt, 1956; Parzen, 1962).
dotsViolin, an R package (R Core Team, 2023) uses gridExtra (Auguie, 2017), gtools (Bolker et al., 2022), tidyr (Wickham et al., 2023c), stringr (Wickham, 2022), dplyr (Wickham et al., 2023b), ggplot2 (Wickham et al., 2023a), lazyeval (Wickham, 2019), magrittr (Bache and Wickham, 2022), rlang (Henry and Wickham, 2023), scales (Wickham and Seidel, 2022), tidyselect (Henry and Wickham, 2022)
Documentation was written with R-packages roxygen2 (Wickham et al., 2022), knitr (Xie, 2023), Rmarkdown (Allaire et al., 2023).
Academic presentation related (Roa-Ovalle, 2019)
devtools::install_gitlab(repo = "ferroao/dotsViolin")To cite package ‘dotsViolin’ in publications use:
Roa-Ovalle F, Telles M (2023). dotsViolin: Integrated tables in dot and violin R ggplots. R package version 0.0.1, https://gitlab.com/ferroao/dotsViolin.
To write citation to file:
sink("dotsViolin.bib")
toBibtex(citation("dotsViolin"))
sink()Fernando
Roa
Mariana PC
Telles
Define your plotting window size with something like
par(pin=c(10,6)), or with svg(),
png(), etc.
In VSCode, you could use something like this
{
"r.plot.useHttpgd": false,
"r.plot.devArgs": {
"width": 800,
"height": 600
}
}library(dotsViolin)
fabaceae_mode_counts <- get_modes_counts(fabaceae_clade_n_df, "clade", "parsed_n")fabaceae_mode_counts| clade | m1 | m2 | m3 | count |
|---|---|---|---|---|
| Caesalpinieae | 12 | NA | NA | 29 |
| Cassieae | 14 | 8 | 12 | 64 |
| Cercidoideae | 14 | 7 | NA | 33 |
| Detarioideae | 12 | 8,17 | NA | 50 |
| Dialioideae | 14 | NA | NA | 6 |
| Dimorphandra and rel. | 14 | 13 | NA | 16 |
| Mimosoids | 13 | 26 | 14 | 221 |
| outgroup | 8 | 12 | 11 | 145 |
| Papilionoideae | 8 | 11 | 7 | 1410 |
| Umtiza and rel. | 14 | NA | NA | 7 |
library(dotsViolin)
fabaceae_clade_n_df_count <- make_legend_with_stats(fabaceae_mode_counts, "label_count", 1, TRUE)
fabaceae_clade_n_df$label_count <- fabaceae_clade_n_df_count$label_count[match(
fabaceae_clade_n_df$clade,
fabaceae_clade_n_df_count$clade
)]
desiredorder1 <- unique(fabaceae_clade_n_df$clade)fabaceae_clade_n_df
tip.label clade parsed_n
1 KX374504_Abarema_centiflora Mimosoids 13
2 KX213142_Adenodolichos_bussei Papilionoideae 11
3 KX792912_Almaleea_cambagei Papilionoideae 8
4 KP109982_Amphithalea_cymbifolia Papilionoideae 9
5 KP230727_Argyrolobium_tuberosum Papilionoideae 13
6 GU220019_Ateleia_arsenii Papilionoideae 14
label_count
1 Mimosoids 13 26 14 (221)
2 Papilionoideae 8 11 7 (1410)
3 Papilionoideae 8 11 7 (1410)
4 Papilionoideae 8 11 7 (1410)
5 Papilionoideae 8 11 7 (1410)
6 Papilionoideae 8 11 7 (1410)par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_n_df, "clade", "label_count", "parsed_n", 2,
30, "Chromosome haploid number", desiredorder1, 1, .85, 4,
"ownwork",
violin = FALSE
)
par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_n_df, "clade", "label_count", "parsed_n", 2,
30, "Chromosome haploid number", desiredorder1, 1, .85, 4,
dots = FALSE
)
par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_n_df, "clade", "label_count", "parsed_n", 2,
30, "Chromosome haploid number", desiredorder1, 1, .85, 4
)
Define your plotting window size with something like
par(pin=c(10,6)), or with svg(),
png(), etc.
library(dotsViolin)
fabaceae_Cx_peak_counts_per_clade_df <- get_peaks_counts_continuous(
fabaceae_clade_1Cx_df,
"clade", "Cx", 2, 0.25, 1, 2
)fabaceae_Cx_peak_counts_per_clade_df| clade | m1 | m2 | counts | |
|---|---|---|---|---|
| Caesalpinieae | Caesalpinieae | 0.85,1.80 | 2 | |
| Cassieae | Cassieae | 0.69 | 0.52,0.56 | 6 |
| Cercidoideae | Cercidoideae | 0.60 | 5 | |
| COM clade | COM clade | 0.35,0.50,0.83 | 3 | |
| Detarioideae | Detarioideae | 2.21 | 0.84,2.01 | 4 |
| Dimorphandra & rel. | Dimorphandra & rel. | 0.73,0.79 | 2 | |
| Malvids | Malvids | 0.40 | 0.63 | 8 |
| Mimosoids | Mimosoids | 0.70 | 0.43 | 42 |
| outgroups | outgroups | 0.48 | 1.38,2.76 | 9 |
| Papilionoideae | Papilionoideae | 0.59 | 212 | |
| Polygala amara | Polygala amara | 0.42 | 1 | |
| Umtiza & rel. | Umtiza & rel. | 0.65,1.05 | 2 | |
| Vitis vinifera | Vitis vinifera | 0.43 | 1 |
library(dotsViolin)
namecol <- "labelcountcustom"
fabaceae_clade_1Cx_modes_count_df <- make_legend_with_stats(
fabaceae_Cx_peak_counts_per_clade_df,
namecol, 1, TRUE
)
fabaceae_clade_1Cx_df$labelcountcustom <-
fabaceae_clade_1Cx_modes_count_df$labelcountcustom[match(
fabaceae_clade_1Cx_df$clade,
fabaceae_clade_1Cx_modes_count_df$clade
)]
desiredorder <- unique(fabaceae_clade_1Cx_df$clade)fabaceae_clade_1Cx_df
name clade Cx genus ownwork
6 'Silene_latifolia_JF715055' outgroups 2.7000 Silene no
7 'Fagopyrum_esculentum_NC010776' outgroups 1.4350 Fagopyrum no
11 'Helianthus_annuus_NC007977' outgroups 2.4250 Helianthus no
12 'Daucus_carota_NC008325' outgroups 2.8375 Daucus no
14 'Olea_europaea_NC013707' outgroups 1.9500 Olea no
18 'Coffea_arabica_NC008535' outgroups 0.6000 Coffea no
labelcountcustom
6 outgroups 0.48 1.38,2.76 (9)
7 outgroups 0.48 1.38,2.76 (9)
11 outgroups 0.48 1.38,2.76 (9)
12 outgroups 0.48 1.38,2.76 (9)
14 outgroups 0.48 1.38,2.76 (9)
18 outgroups 0.48 1.38,2.76 (9)par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_1Cx_df, "clade", "labelcountcustom", "Cx", 3,
3, "Genome Size", desiredorder, 0.03, 0.25, 2,
"ownwork"
)
par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_1Cx_df, "clade", "labelcountcustom", "Cx", 3,
3, "Genome Size", desiredorder, 0.03, 0.25, 2,
dots = FALSE
)
par(mar = c(0, 0, 0, 0), omi = rep(0, 4))
dots_and_violin(
fabaceae_clade_1Cx_df, "clade", "labelcountcustom", "Cx", 3,
3, "Genome Size", desiredorder, 0.03, 0.25, 2,
"ownwork",
violin = FALSE
)