Removed X rows containing missing values. Why?! Impossible!!

[niko_bio]

Hi!

I'm getting very confused as to why rows seems to be removed when they shouldn't be when I plot them. The y-values range from 1 to 8, but when I create the diagram, it plots from 0 to 10. If I change it to ylim(1-8) I get this error. Why?!

Here's my full data and the plot:

data.frame(
stringsAsFactors = FALSE,
species = c("Acraea issoria",
"Athyma asura","Athyma cama","Athyma orientalis",
"Athyma selenophora","Atrophaneura aidoneus","Bibasis vasutana",
"Byasa crassipes","Byasa polyeuctes","Cethosia biblis",
"Cyrestis thyodamas","Danaus genutia","Delias pasithoe",
"Dichorragia nesimachus","Dodona adonira","Euploea eunice",
"Euploea mulciber","Euthalia iva","Euthalia lubentina",
"Graphium agamemnon","Graphium agetes",
"Graphium chironides","Graphium cloanthus","Graphium doson",
"Graphium leechi","Graphium sarpedon","Hebomoia glaucippe",
"Heliophorus brahma","Hestina assimilis",
"Hypolimnas bolina","Junonia almana","Junonia atlites","Junonia orithya",
"Kaniska canace","Lamproptera curius","Lethe confusa",
"Lethe dura","Lethe sinorix","Lethe verma",
"Melanitis leda","Neope armandii","Neope pulaha",
"Neorina patria","Neptis hylas","Pachliopta aristolochiae",
"Papilio arcturus","Papilio bianor","Papilio demoleus",
"Papilio helenus","Papilio memnon","Papilio nephelus",
"Papilio paris","Papilio polytes","Papilio protenor",
"Parantica sita","Parasarpa dudu","Pieris canidia",
"Pieris rapae","Polyura dolon","Prioneris thestylis",
"Pseudergolis wedah","Stibochiona nicea","Sumalia daraxa",
"Symbrenthia lilaea","Troides aeacus","Vanessa cardui",
"Vanessa indica","Vindula erota","Zemeros flegyas"),
n = c(1,7,7,7,1,7,1,6,7,8,1,
7,7,1,1,1,7,1,3,1,6,2,6,1,7,7,6,1,7,7,
2,4,2,2,2,1,1,2,7,7,1,3,1,7,8,7,7,1,7,
5,2,7,6,7,2,4,6,1,5,1,7,3,7,7,5,1,6,7,
2),
Family = c("Nymphalidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Nymphalidae",
"Papilionidae","Hesperiidae","Papilionidae","Papilionidae",
"Nymphalidae","Nymphalidae","Nymphalidae","Pieridae",
"Nymphalidae","Riodinidae","Nymphalidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Papilionidae","Papilionidae",
"Papilionidae","Papilionidae","Papilionidae",
"Papilionidae","Papilionidae","Pieridae","Lycaenidae",
"Nymphalidae","Nymphalidae","Nymphalidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Papilionidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Nymphalidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Nymphalidae",
"Nymphalidae","Papilionidae","Papilionidae","Papilionidae",
"Papilionidae","Papilionidae","Papilionidae",
"Papilionidae","Papilionidae","Papilionidae","Papilionidae",
"Nymphalidae","Nymphalidae","Pieridae","Pieridae",
"Nymphalidae","Pieridae","Nymphalidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Papilionidae","Nymphalidae",
"Nymphalidae","Nymphalidae","Riodinidae"),
Individuals = c(33,411,293,277,16,103,13,
69,291,1143,13,1425,355,32,11,40,3588,13,26,
15,43,60,116,3,454,152,52,4,637,201,56,111,
59,24,72,15,8,13,123,196,7,40,42,71,2844,107,
1760,7,414,87,45,900,23,2737,289,93,152,51,
71,62,153,51,114,160,47,51,124,170,48),
indi_logged = c(3.49650756146648,
6.01859321449623,5.68017260901707,5.62401750618734,2.77258872223978,
4.63472898822964,2.56494935746154,4.23410650459726,
5.67332326717149,7.04141166379481,2.56494935746154,
7.26192709270275,5.87211778947542,3.46573590279973,
2.39789527279837,3.68887945411394,8.18535022317869,
2.56494935746154,3.25809653802148,2.70805020110221,
3.76120011569356,4.0943445622221,4.75359019110636,1.09861228866811,
6.11809719804135,5.02388052084628,3.95124371858143,
1.38629436111989,6.45676965557216,5.30330490805908,
4.02535169073515,4.70953020131233,4.07753744390572,
3.17805383034795,4.27666611901606,2.70805020110221,
2.07944154167984,2.56494935746154,4.81218435537242,
5.27811465923052,1.94591014905531,3.68887945411394,3.73766961828337,
4.26267987704132,7.95296679092313,4.67282883446191,
7.4730690880322,1.94591014905531,6.02586597382531,
4.46590811865458,3.80666248977032,6.80239476332431,
3.13549421592915,7.91461770904068,5.66642668811243,
4.53259949315326,5.02388052084628,3.93182563272433,
4.26267987704132,4.12713438504509,5.03043792139244,3.93182563272433,
4.7361984483945,5.07517381523383,3.85014760171006,
3.93182563272433,4.82028156560504,5.13579843705026,
3.87120101090789)
)

And here's my plot function:

spx2 <- ggscatter(data_2_mod, x="indi_logged", y="n", add="reg.line", add.params = list(color="blue", fill="lightgray"),
conf.int=TRUE) + ylab("n") + xlab("indi_logged") +
ggtitle(expression(atop(bold("individuals (per species) vs. replicates"), atop(italic("Extracted data"))))) +
theme(plot.title = element_text(color="#993333", size=14, face="bold", hjust = 0.5))
spx2 + stat_cor(method="pearson", label.x =3, label.y = 7)
spx2 + stat_cor(p.accuracy = 0.001, r.accuracy = 0.01, label.x=3, label.y = 9)

[nirgrahamuk]

I don't see that you provided code that attempts to set the y axis limits, so I can't judge it for you.
You can try this though, as I believe it achieves your goal.

ggpar(spx2,
      ylim = c(1,8))

[niko_bio]

Hello!

I tried your solution but it still doesn't work. I get the same errors (i.e., rows being removed without reason).

[nirgrahamuk]

Your original code as shared does not show any rows removal message, and my fix (for adjusting the axis) does not introduce any such message either. (at least on my laptop with my setup, which we can discuss if we can't identify any other difference).

Perhaps what you shared doesn't reflect the problematic data you have ? Is the data_2mod you shared identical with what is causing you issues, or is it a sample from it that doesn't illustrate the issue ?

[niko_bio]

The error pops up as soon as I add the "ylim(1,8)". I am running the exact code posted here.

Try to run my code above but add that line also.

See my picture here:

[nirgrahamuk]

You arent using ggpar. I used ggpar. Thats the difference...

[niko_bio]

Thank you. Using the ggpar command, the error doesnt show up (If I remember, I did try it the first time around when you first posted, but it didn't work back then. Now it does though...). But I still don't understand the logics behind it, i.e. why is the error message showing up in the first place when there are no values lower than 1 or higher than 8.