Hello everyone, I hope you are very well. Does anyone know how I could improve my boxplot? The boxplots on the right don't look good. Maybe I could zoom in on those boxplots or change the Y axis? I would appreciate if you could help me know how to do it.
library(readxl)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(reshape2)
library(ggpubr)
#> Loading required package: ggplot2
library(readr)
library(ggplot2)
library(plyr)
#> ------------------------------------------------------------------------------
#> You have loaded plyr after dplyr - this is likely to cause problems.
#> If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
#> library(plyr); library(dplyr)
#> ------------------------------------------------------------------------------
#>
#> Attaching package: 'plyr'
#> The following object is masked from 'package:ggpubr':
#>
#> mutate
#> The following objects are masked from 'package:dplyr':
#>
#> arrange, count, desc, failwith, id, mutate, rename, summarise,
#> summarize
getwd()
#> [1] "C:/Users/Osiris Díaz Torres/AppData/Local/Temp/RtmpuSXnbo/reprex532835016a58"
osiris_data <- data.frame (tibble::tribble(
~Month, ~index, ~Denitrification, ~Nitrogen_Fixation, ~COMAMMOX, ~Dissimilatoria, ~Assimilatoria, ~ANAMMOX, ~Nitrification,
"July", "1A", 241083L, 78096L, 19922L, 38184L, 2723L, 6222L, 6701L,
"July", "1B", 131841L, 21618L, 3629L, 12166L, 1390L, 4098L, 1216L,
"July", "1C", 80748L, 33396L, 3569L, 25013L, 1696L, 1365L, 1327L,
"August", "1D", 13172L, 7158L, 11078L, 30952L, 1846L, 785L, 5553L,
"August", "1E", 14113L, 16658L, 5517L, 27611L, 7344L, 2448L, 2857L,
"August", "1F", 44051L, 45890L, 10043L, 36583L, 12601L, 10463L, 5815L,
"September", "1G", 22360L, 7475L, 1342L, 5391L, 1368L, 3635L, 508L,
"September", "1H", 61649L, 17314L, 9888L, 31348L, 3413L, 8750L, 3487L,
"July", "2A", 470403L, 280308L, 12015L, 36603L, 10899L, 16560L, 4284L,
"July", "2B", 344418L, 210774L, 9872L, 27000L, 4861L, 10166L, 3113L,
"July", "2C", 432009L, 111588L, 6398L, 16559L, 4546L, 15229L, 2293L,
"August", "2D", 15574L, 13821L, 5765L, 18341L, 2979L, 2603L, 3051L,
"August", "2E", 33508L, 11271L, 7014L, 37096L, 7178L, 7032L, 3511L,
"August", "2F", 20538L, 8293L, 2463L, 11168L, 2302L, 4863L, 1259L,
"September", "2G", 71801L, 15902L, 7032L, 46496L, 4005L, 9702L, 2514L,
"September", "2H", 74872L, 20621L, 6123L, 24425L, 8274L, 12343L, 2526L,
"July", "3A", 166374L, 91140L, 6618L, 43272L, 5825L, 4516L, 2332L,
"July", "3B", 6822L, 32178L, 671L, 959L, 2472L, 214L, 256L,
"July", "3C", 69876L, 16068L, 1776L, 7197L, 1425L, 2569L, 635L,
"August", "3D", 10648L, 1948L, 2498L, 8252L, 918L, 2190L, 1246L,
"August", "3E", 17522L, 13002L, 2949L, 13478L, 3230L, 3939L, 1516L,
"August", "3F", 13806L, 10451L, 2751L, 10064L, 2406L, 3153L, 1506L,
"September", "3G", 16436L, 12497L, 2401L, 10332L, 3659L, 2859L, 971L,
"September", "3H", 3393L, 707L, 672L, 1777L, 44L, 418L, 235L,
"July", "4A", 464913L, 714936L, 27599L, 90008L, 25119L, 17040L, 9996L,
"July", "4B", 360375L, 64410L, 5477L, 11774L, 3380L, 12865L, 2145L,
"July", "4C", 161214L, 52884L, 1866L, 5996L, 1685L, 5818L, 649L,
"August", "4D", 27033L, 21631L, 4287L, 17761L, 5088L, 6050L, 2384L,
"August", "4E", 25259L, 29283L, 5168L, 22521L, 6911L, 5580L, 2744L,
"August", "4F", 1061L, 315L, 200L, 823L, 148L, 292L, 100L,
"September", "4G", 46091L, 11926L, 6268L, 54813L, 5440L, 4198L, 2266L,
"September", "4H", 181927L, 49926L, 41028L, 120533L, 8368L, 22528L, 14641L,
"July", "5A", 98574L, 52422L, 15821L, 32423L, 4425L, 1809L, 5293L,
"July", "5B", 76164L, 39006L, 6777L, 18842L, 3723L, 2048L, 2275L,
"July", "5C", 18999L, 20400L, 2928L, 5466L, 162L, 314L, 976L,
"August", "5D", 34831L, 7153L, 3203L, 9836L, 1833L, 7938L, 1728L,
"August", "5E", 39710L, 9407L, 3564L, 33915L, 2266L, 7788L, 1838L,
"August", "5F", 50735L, 15063L, 13134L, 36511L, 3030L, 10037L, 6800L,
"September", "5G", 15822L, 11090L, 8181L, 26025L, 4015L, 1014L, 2977L,
"September", "5H", 21022L, 6920L, 5870L, 24763L, 8597L, 4756L, 2057L,
"July", "6A", 571743L, 392658L, 20613L, 55042L, 14212L, 19138L, 7140L,
"July", "6B", 541449L, 106320L, 15660L, 30734L, 5892L, 17887L, 5573L,
"July", "6C", 127176L, 75582L, 4302L, 11443L, 2975L, 4302L, 1503L,
"August", "6D", 32901L, 4651L, 2097L, 12039L, 1771L, 7261L, 1083L,
"August", "6E", 19284L, 27733L, 3983L, 19887L, 6159L, 4127L, 2028L,
"August", "6F", 42780L, 32950L, 6359L, 23536L, 7175L, 10080L, 3609L,
"September", "6G", 12144L, 5690L, 2501L, 12445L, 2671L, 3102L, 927L,
"September", "6H", 141787L, 36553L, 11574L, 51092L, 11862L, 23236L, 4178L,
"July", "7A", 283032L, 112584L, 41889L, 75690L, 4617L, 4223L, 14008L,
"July", "7B", 65367L, 10440L, 2466L, 17990L, 1338L, 962L, 822L,
"July", "7C", 120444L, 29124L, 1650L, 15250L, 619L, 3320L, 549L,
"August", "7D", 89190L, 15278L, 4715L, 22381L, 4028L, 20359L, 2411L,
"August", "7E", 43504L, 19521L, 14184L, 41422L, 3992L, 7762L, 7330L,
"September", "7F", 64119L, 21059L, 18630L, 52539L, 2617L, 6595L, 6516L,
"September", "7G", 10429L, 5454L, 4146L, 12557L, 2494L, 1262L, 1522L,
"September", "7H", 5129L, 2403L, 1727L, 6686L, 1799L, 861L, 606L,
"July", "8A", 462741L, 229458L, 15117L, 37010L, 7960L, 15889L, 5272L,
"July", "8B", 629298L, 316728L, 21951L, 54069L, 13955L, 21074L, 8134L,
"July", "8C", 241308L, 48078L, 1784L, 6312L, 1804L, 8843L, 580L,
"August", "8D", 38784L, 51522L, 10419L, 42499L, 14030L, 8433L, 5892L,
"August", "8E", 23091L, 31601L, 10168L, 32022L, 6545L, 4486L, 5575L,
"September", "8F", 120124L, 42674L, 24377L, 67537L, 8433L, 15701L, 9097L,
"September", "8G", 40738L, 27149L, 16765L, 55953L, 11402L, 3624L, 6269L,
"September", "8H", 75578L, 22411L, 22493L, 60891L, 4108L, 7574L, 7986L,
"July", "9A", 76770L, 18144L, 4995L, 24532L, 2403L, 1284L, 1664L,
"July", "9B", 174456L, 86358L, 10913L, 35759L, 6762L, 5967L, 3772L,
"July", "9C", 67851L, 14352L, 5745L, 9217L, 800L, 1683L, 1916L,
"August", "9D", 42805L, 50516L, 10053L, 49053L, 17173L, 8950L, 5454L,
"August", "9E", 69634L, 32788L, 30904L, 87404L, 4784L, 11788L, 15632L,
"September", "9F", 123576L, 26060L, 9273L, 36769L, 10477L, 20119L, 3435L,
"September", "9G", 10169L, 7110L, 3638L, 10558L, 2636L, 1197L, 1407L,
"September", "9H", 6250L, 22375L, 1567L, 5450L, 12910L, 878L, 625L,
"July", "10A", 270771L, 56214L, 5459L, 14087L, 3907L, 9721L, 2065L,
"July", "10B", 382572L, 60084L, 3899L, 9658L, 2689L, 13771L, 1478L,
"July", "10C", 63942L, 45228L, 3995L, 8388L, 1270L, 2034L, 1412L,
"August", "10D", 41210L, 7789L, 2310L, 11275L, 1492L, 9209L, 1145L,
"August", "10E", 20508L, 21164L, 4475L, 17130L, 4205L, 4181L, 2389L,
"September", "10F", 71491L, 16999L, 3253L, 12666L, 3192L, 11748L, 1218L,
"September", "10G", 10921L, 4050L, 3674L, 10800L, 1230L, 1164L, 1351L,
"September", "10H", 14495L, 3438L, 2099L, 6120L, 720L, 1998L, 738L,
"July", "11A", 14121L, 7746L, 1337L, 3596L, 473L, 426L, 445L,
"July", "11B", 21300L, 4344L, 870L, 1925L, 248L, 711L, 291L,
"July", "11C", 125088L, 39912L, 12954L, 24066L, 1455L, 2736L, 4322L,
"August", "11D", 28491L, 36508L, 7067L, 30884L, 11100L, 6210L, 3844L,
"August", "11E", 39719L, 18589L, 5539L, 19519L, 4599L, 8974L, 3039L,
"September", "11F", 25299L, 3320L, 2892L, 14885L, 1057L, 3334L, 1008L,
"September", "11G", 4937L, 2940L, 2252L, 8834L, 1856L, 473L, 817L,
"September", "11H", 44171L, 8419L, 4736L, 39033L, 5131L, 6143L, 1658L,
"July", "12A", 714789L, 93714L, 4965L, 12620L, 3330L, 26322L, 1796L,
"July", "12B", 286134L, 105462L, 7295L, 18425L, 3208L, 9662L, 2488L,
"August", "12C", 69297L, 13236L, 2540L, 9749L, 2308L, 16296L, 1313L,
"August", "12D", 34538L, 24326L, 18989L, 56234L, 8311L, 5586L, 10065L,
"August", "12E", 24813L, 7898L, 6477L, 23042L, 2320L, 4367L, 3257L,
"September", "12F", 69957L, 28268L, 6039L, 25968L, 7798L, 10893L, 2186L,
"September", "12G", 135130L, 47669L, 37944L, 105122L, 13137L, 16548L, 13979L,
"September", "12H", 95766L, 29479L, 10788L, 41605L, 14881L, 16716L, 4190L
)
)
osiris_data <- data.frame(read_delim("osiris_data_nitrogeno.txt",
"\t", escape_double = FALSE, trim_ws = TRUE))
#> Error: 'osiris_data_nitrogeno.txt' does not exist in current working directory ('C:/Users/Osiris Díaz Torres/AppData/Local/Temp/RtmpuSXnbo/reprex532835016a58').
head(osiris_data)
#> Month index Denitrification Nitrogen_Fixation COMAMMOX Dissimilatoria
#> 1 July 1A 241083 78096 19922 38184
#> 2 July 1B 131841 21618 3629 12166
#> 3 July 1C 80748 33396 3569 25013
#> 4 August 1D 13172 7158 11078 30952
#> 5 August 1E 14113 16658 5517 27611
#> 6 August 1F 44051 45890 10043 36583
#> Assimilatoria ANAMMOX Nitrification
#> 1 2723 6222 6701
#> 2 1390 4098 1216
#> 3 1696 1365 1327
#> 4 1846 785 5553
#> 5 7344 2448 2857
#> 6 12601 10463 5815
osiris_data <- osiris_data[,-2]
head(osiris_data)
#> Month Denitrification Nitrogen_Fixation COMAMMOX Dissimilatoria
#> 1 July 241083 78096 19922 38184
#> 2 July 131841 21618 3629 12166
#> 3 July 80748 33396 3569 25013
#> 4 August 13172 7158 11078 30952
#> 5 August 14113 16658 5517 27611
#> 6 August 44051 45890 10043 36583
#> Assimilatoria ANAMMOX Nitrification
#> 1 2723 6222 6701
#> 2 1390 4098 1216
#> 3 1696 1365 1327
#> 4 1846 785 5553
#> 5 7344 2448 2857
#> 6 12601 10463 5815
data_transformed = melt(data = osiris_data, id.vars = c("Month"))
head(data_transformed)
#> Month variable value
#> 1 July Denitrification 241083
#> 2 July Denitrification 131841
#> 3 July Denitrification 80748
#> 4 August Denitrification 13172
#> 5 August Denitrification 14113
#> 6 August Denitrification 44051
table(data_transformed$Month, data_transformed$variable)
#>
#> Denitrification Nitrogen_Fixation COMAMMOX Dissimilatoria
#> August 31 31 31 31
#> July 35 35 35 35
#> September 30 30 30 30
#>
#> Assimilatoria ANAMMOX Nitrification
#> August 31 31 31
#> July 35 35 35
#> September 30 30 30
ddply(data_transformed,~variable,summarise,
suma = sum(value))%>% arrange(desc(suma))
#> variable suma
#> 1 Denitrification 10983858
#> 2 Nitrogen_Fixation 4797066
#> 3 Dissimilatoria 2633676
#> 4 COMAMMOX 811883
#> 5 ANAMMOX 707387
#> 6 Assimilatoria 481914
#> 7 Nitrification 326590
head(data_transformed)
#> Month variable value
#> 1 July Denitrification 241083
#> 2 July Denitrification 131841
#> 3 July Denitrification 80748
#> 4 August Denitrification 13172
#> 5 August Denitrification 14113
#> 6 August Denitrification 44051
data_transformed$Month <- factor(data_transformed$Month, levels = c("July", "August", "September"))
ggplot(data_transformed, aes(x = variable, y = value, fill = Month))+
coord_cartesian(ylim=c(0,700000))+
geom_boxplot() + geom_point(position = position_dodge(width = 0.75), alpha = 0.1) +
theme_classic() + xlab("") + ylab("Counts")+
theme(axis.text.x = element_text(angle =45, vjust = 0.6))
Created on 2021-07-11 by the reprex package (v0.3.0)