Plotting a box plot from a table with 7 columns

Question

I am trying to plot the following data (paste-bin link) https:[enter image description here][1]//pastebin.com/w1WaEcPd as a box plot with the trinucleotide identity as the x column and the Frequency as the y column. I have attached a picture of the graph I am envisioning and the code I have so far. I am getting the error:

"Error in FUN(X[[i]], ...) : object 'gene' not found".

library(ggplot2)
library(dplyr)
library(tidyr)
library(stringr)

marte <- tribble(
  ~gene, ~funnyName1, ~funnyName2, ~funnyName3, ~funnyName4, ~funnyName5, ~funnyName6, ~control
  "AAA",  0.021383202,    0.016654469,    0.022484448,    0.025311535,   0.025495724,    0.02017925, 0.024144802,  
  "TAG",  0.019927531,    0.018790672,    0.015649845,    0.02230479, 0.019363723,    0.02017925 , 0.013676519, 
  "AGC",  0.013209711,    0.016891825,    0.014520044,    0.014302046,    0.014804269,    0.012904701 , 0.016027898,
  "TGT",  0.033757832,    0.034990209,    0.031899462,    0.034446096,    0.034475058,    0.031047513 , 0.027512454,
  "GAT",  0.013006661,    0.007615167,    0.009163947,    0.010540757,    0.008234933,    0.012000828 , 0.01232813,
  "CAC",  0.011210666,    0.015012758,    0.01241387, 0.011478221,    0.011045046,    0.013579884 , 0.014466955,
  "GGG",  0.012712095,    0.011927132,    0.013222864,    0.011558249,    0.014292494,    0.014647108 , 0.014706078, 
  "CGA",  0.00230219, 0.000969203,    0.001325076,    0.002034983,    0.001656292,    0.002036438 , 0.002198605,
  "TCG",  0.004169681,    0.007377811,    0.005649008,    0.005133189,    0.006057561,    0.006131094 , 0.002630355,
  "ACA",  0.011259284,    0.013825979,    0.010656401,    0.009900537,    0.010617015,    0.009670358 , 0.017110594,
  "TTT",  0.033305974,    0.04751073, 0.043476442,    0.035212073,    0.037359611,    0.043669073 , 0.037754899,
  "ATC",  0.01259198, 0.013905097,    0.013222864,    0.013501772,    0.012087207,    0.010356431 , 0.010269014,
  "CCC",  0.009591983,    0.004213066,    0.006764862,    0.010506459,    0.006560031,    0.009354547 , 0.015795417,
  "GCT",  0.021391781,    0.025397077,    0.022972634,    0.024545558,    0.023513757,    0.024426367 , 0.019063434,
  "CTA",  0.012680636,    0.011848013,    0.013976065,    0.01610838, 0.014794964,    0.016128154 , 0.011570907,
  "GTG",  0.018394644,    0.015507249,    0.01591486, 0.01932091, 0.019856889,    0.017086478 , 0.020245766,
  "GGA",  0.017702557,    0.014182012,    0.018871872,    0.017926146,    0.018237817,    0.016411295 , 0.015895051,
  "CGG",  0.00377216, 0.00346144, 0.003361509,    0.00339545, 0.004029069,    0.004258007 , 0.002889406,
  "GAC",  0.019684443,    0.018790672,    0.025469356,    0.02854693, 0.027663791,    0.02270574 , 0.010773829,
  "CAT",  0.015297412,    0.014083114,    0.01355762, 0.013879044,    0.013771413,    0.01256711 , 0.016114248, 
  "AGT",  0.018391784,    0.013054572,    0.012288337,    0.018532068,    0.014376239,    0.014745119 , 0.018087014,
  "TGC",  0.020382249,    0.025041043,    0.02170335, 0.02225906, 0.021708586,    0.02506888 , 0.018425772, 
  "AAG",  0.016818859,    0.011393081,    0.018258153,    0.016920087,    0.016293071,    0.01251266 , 0.018731318,
  "TAA",  0.016710184,    0.019324723,    0.023697938,    0.021150109,    0.0213643,  0.019351607 , 0.016067752, 
  "CTG",  0.034733046,    0.040864767,    0.036265238,    0.035143478,    0.036084824,    0.035555991 , 0.02738625, 
  "GTA",  0.014556707,    0.012560081,    0.012706782,    0.014667886,    0.014320409,    0.013863025 , 0.011776818, 
  "CCT",  0.015168718,    0.012184267,    0.012818367,    0.010735109,    0.012264002,    0.010988054 , 0.021819993, 
  "GCC",  0.009183023,    0.007239354,    0.00776913, 0.007808391,    0.008197713,    0.007198319 , 0.013530389, 
  "TTC",  0.018537637,    0.015922622,    0.018244205,    0.015639648,    0.017967972,    0.02003768 , 0.020591166, 
  "ATT",  0.018097218,    0.017069842,    0.014743214,    0.015045158,    0.017204961,    0.017184488 , 0.018425772, 
  "TCA",  0.015606277,    0.012757877,    0.013794739,    0.013936207,    0.011510296,    0.010323761 , 0.01798738, 
  "ACG",  0.003929453,    0.002650474,    0.00380785, 0.003829885,    0.003535903,    0.003528374 , 0.002789771, 
  "CCA",  0.013678729,    0.010601895,    0.016012498,    0.012964445,    0.014004038,    0.013340303 , 0.017369645, 
  "GCG",  0.001401333,    0.000929644,    0.000864786,    0.00050303, 0.00042803, 0.000457382 , 0.002504151, 
  "CTC",  0.021940875,    0.01946318, 0.021215164,    0.02198468, 0.022145921,    0.026560815 , 0.019262703, 
  "GTT",  0.019249743,    0.023537789,    0.020141155,    0.020967189,    0.019614959,    0.020854433 , 0.017827964, 
  "TCT",  0.032416556,    0.033704532,    0.033405864,    0.032696925,    0.034102858,    0.037919131 , 0.025539688, 
  "ACC",  0.011316481,    0.013034792,    0.015133763,    0.011775466,    0.012384967,    0.013547214 , 0.011697111, 
  "TTG",  0.029728284,    0.040330716,    0.03107652, 0.030993483,    0.031739385,    0.03275725 , 0.02247094, 
  "ATA",  0.011276443,    0.010839251,    0.011395654,    0.008402881,    0.010635625,    0.013971925 , 0.013457323, 
  "GAG",  0.011645365,    0.009454675,    0.007992301,    0.009397508,    0.008830453,    0.00750324 , 0.016745267, 
  "CAA",  0.009388933,    0.007536048,    0.010935364,    0.008208529,    0.009658599,    0.009332767 , 0.013955497, 
  "GGT",  0.010687311,    0.012738098,    0.00974977, 0.008711558,    0.01001219, 0.010977164 , 0.013556958, 
  "CGC",  0.001201143,    0.001305457,    0.001325076,    0.001017492,    0.001079381,    0.001785967 , 0.00212554, 
  "AAC",  0.013266908,    0.019146706,    0.015747482,    0.013193095,    0.014962454,    0.014418417 , 0.012441049, 
  "TAT",  0.012557662,    0.011630437,    0.011814099,    0.011924088,    0.011435856,    0.011761247 , 0.01454002, 
  "AGA",  0.019558609,    0.019502739,    0.017477055,    0.01982394, 0.017716737,    0.016160824 , 0.019667884, 
  "TGG",  0.024234486,    0.028818957,    0.02414428, 0.024111124,    0.023439317,    0.024143226 , 0.021766855, 
  "TTA",  0.015523341,    0.018493977,    0.01705861, 0.019572425,    0.016311681,    0.013111612 , 0.017827964, 
  "ATG",  0.014385115,    0.006903099,    0.013153123,    0.013593232,    0.011742921,    0.012175068 , 0.016917967, 
  "TCC",  0.014041931,    0.007872303,    0.00974977, 0.009671888,    0.009798174,    0.009909939 , 0.016898041, 
  "ACT",  0.027183006,    0.030045295,    0.031020727,    0.034777638,    0.034130773,    0.033987825 , 0.016446363, 
  "CTT",  0.02351094, 0.027256364,    0.026766536,    0.025631645,    0.02585862, 0.025656942 , 0.02465626, 
  "GTC",  0.012952323,    0.012678759,    0.008745502,    0.008814451,    0.008076748,    0.00761214 , 0.012965792, 
  "CCG",  0.002599616,    0.00114722, 0.002189862,    0.001783469,    0.002149457,    0.003081882 , 0.002949186, 
  "GCA",  0.013684448,    0.02231145, 0.016486735,    0.016005488,    0.01599531, 0.018817995 , 0.014792428, 
  "AGG",  0.014244982,    0.008722828,    0.013334449,    0.012381388,    0.012766472,    0.010770253 , 0.018113584, 
  "TGA",  0.025881768,    0.019008248,    0.023098167,    0.023848177,    0.025532944,    0.023500713 , 0.0193092, 
  "AAT",  0.016489975,    0.014538046,    0.018788183,    0.014004802,    0.018098242,    0.017881451 , 0.016094321, 
  "TAC",  0.011036214,    0.00860415, 0.008271264,    0.008402881,    0.008635048,    0.011216745 , 0.010355364, 
  "GGC",  0.01302668, 0.014142453,    0.011409602,    0.01280439, 0.011361416,    0.011576116 , 0.013317835, 
  "CGT",  0.004718775,    0.006428388,    0.006346417,    0.004778781,    0.005378295,    0.00509654 , 0.003659914, 
  "GAA",  0.020542402,    0.017841248,    0.018007086,    0.015102321,    0.018247122,    0.016171714 , 0.017230156, 
  "CAG",  0.017162043,    0.018414858,    0.016472787,    0.016531382,    0.014981064,    0.014244177, 0.022743275
)
colnames(marte) <- c("gene", "a40", "b40", "c40", "a80", "b80", "c80", "control" )

marte %>% pivot_longer(-gene, names_to = "name") %>% 
  mutate(group = if_else(str_detect(name, "40"), "40s", "80s"),
         rep = case_when(
           str_detect(name, "a") ~ "rep1",
           str_detect(name, "b") ~ "rep2",
           str_detect(name, "c") ~ "rep3", 
           TRUE                  ~ NA_character_
         )
  ) %>% 
  ggplot(aes(x = group,  y = value, color = group)) + 
  geom_boxplot() + 
  geom_jitter(alpha = .5) + 
  coord_flip() + 
  facet_wrap(~gene, ncol = 4)

Hi! can you provide a small sample of your data (not via pastebin) but in a copy-pasteable format? For example with the output of `dput(head(marte, 20)`. — Marcelo Avila, Jul 01 '21 at 12:19
Trinucleotide Gene1A Gene2A Gene3A Gene1B Gene2B Gene3B AAA 0.021383202 0.016654469 0.022484448 0.025311535 0.025495724 0.02017925 TAG 0.019927531 0.018790672 0.015649845 0.02230479 0.019363723 0.02017925 AGC 0.013209711 0.016891825 0.014520044 0.014302046 0.014804269 0.012904701 — user14687500, Jul 01 '21 at 12:23
@MarceloAvila The idea is to plot a box plot where Gene 1A&1B are joined together, 2A and 2B together etc... — user14687500, Jul 01 '21 at 12:25
i got the idea, but I would need the data to provide a possible solution. See https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example. So maybe you can edit your question and add at the end the results of `dput(head(marte, 20)`, which will enable us to work with the first 20 rows of "marte", with which we can propose a solution. — Marcelo Avila, Jul 01 '21 at 12:26
great, the formatting of dput() is indeed a bit funny, but as long R interprets it, it is not a problem... another way of presenting the data that is readable in R AND by humans would be recreating a small sample with `tribble` from {dplyr}. but dput is fine, because R reads it and then we can see and manipulate however we want... — Marcelo Avila, Jul 01 '21 at 12:49
@MarceloAvila Okay it's starting to come together. I want to have for each trinucleotide(gene) 3 pairs of boxes so 1 pair for 40s and 80s rep1, 1 pair for 40s and 80s rep2 and 1 pair for 40s and 80s rep3. "Rep" is short for replicate so there are 3 replicates — user14687500, Jul 01 '21 at 13:34
@MarceloAvila Are you able to access this: i.stack.imgur.com/cL4YB.jpg ? It's a rough draft of the kind of graph I was hoping to get — user14687500, Jul 06 '21 at 11:26
@MarceloAvila And I was hoping to combine rep1,2and3 for each group so that I only have 2 boxed (1 red 1 blue) — user14687500, Jul 07 '21 at 21:09

Marcelo Avila · Accepted Answer · 2021-07-09T10:04:57.670

That would be a possible solution using the tidyverse packages. Here I recreated the data table, you would need just to rename the columns and then run the parte with the pivot_longer and mutate to prepare the data for plotting and then plot with ggplot2

I am making a few assumptions here, if it is not exactly what you were thinking, please write a comment.

library(dplyr)
library(ggplot2)
#> Warning: package 'ggplot2' was built under R version 4.1.0
library(tidyr)
library(stringr)

marte <- tribble(
  ~gene, ~funnyName1, ~funnyName2, ~funnyName3, ~funnyName4, ~funnyName5, ~funnyName6,
  "AAA", 0.021383202,   0.016654469, 0.022484448,    0.025311535,   0.025495724,    0.02017925,
  "TAG", 0.019927531,   0.018790672, 0.015649845,    0.02230479,    0.019363723,    0.02017925,
  "AGC", 0.013209711,   0.016891825, 0.014520044,    0.014302046,   0.014804269,    0.012904701,
  "TGT", 0.033757832,   0.034990209, 0.031899462,    0.034446096,   0.034475058,    0.031047513,
  "AAA", 0.013006661,   0.007615167, 0.009163947,    0.010540757,   0.008234933,    0.012000828,
  "TAG", 0.011210666,   0.015012758, 0.01241387,   0.011478221,     0.011045046,    0.013579884,
  "AGC", 0.012712095,   0.011927132, 0.013222864,    0.011558249,   0.014292494,    0.014647108,
  "TGT", 0.00230219 ,   0.000969203, 0.001325076,    0.002034983,   0.001656292,    0.002036438,
  "AAA", 0.004169681,   0.007377811, 0.005649008,    0.005133189,   0.006057561,    0.006131094,
  "TAG", 0.011259284,   0.013825979, 0.010656401,    0.009900537,   0.010617015,    0.009670358,
  "AGC", 0.033305974,   0.04751073,  0.043476442,    0.035212073,   0.037359611,    0.043669073,
  "TGT", 0.01259198 ,   0.013905097, 0.013222864,    0.013501772,   0.012087207,    0.010356431,
  "CCC", 0.009591983,   0.004213066, 0.006764862,    0.010506459,   0.006560031,    0.009354547,
  "GCT", 0.021391781,   0.025397077, 0.022972634,    0.024545558,   0.023513757,    0.024426367,
  "CTA", 0.012680636,   0.011848013, 0.013976065,    0.01610838,    0.014794964,    0.016128154,
  "GTG", 0.018394644,   0.015507249, 0.01591486,   0.01932091,  0.019856889,    0.017086478,
  "GGA", 0.017702557,   0.014182012, 0.018871872,    0.017926146,   0.018237817,    0.016411295,
  "CGG", 0.00377216 ,   0.00346144,  0.003361509,    0.00339545,    0.004029069,    0.004258007
)
colnames(marte) <- c("gene", "a40", "b40", "c40", "a80", "b80", "c80")

marte %>% pivot_longer(-gene, names_to = "name") %>% 
  mutate(group = if_else(str_detect(name, "40"), "group 1", "group 2"),
         rep = case_when(
           str_detect(name, "a") ~ "rep1",
           str_detect(name, "b") ~ "rep2",
           str_detect(name, "c") ~ "rep3", 
           TRUE                  ~ NA_character_
         )
  ) %>% 
  filter(gene %in% c("AAA", "TAG", "AGC", "TGT")) %>% 
  
  ggplot(aes(x = rep, y = value, color = group)) + 
  geom_boxplot() + 
  coord_flip() + 
  facet_wrap(~gene, ncol = 1)

^{Created on 2021-07-01 by the reprex package (v2.0.0)}

Edit

marte %>% pivot_longer(-gene, names_to = "name") %>% 
  mutate(group = if_else(str_detect(name, "40"), "40s", "80s"),
         rep = case_when(
           str_detect(name, "a") ~ "rep1",
           str_detect(name, "b") ~ "rep2",
           str_detect(name, "c") ~ "rep3", 
           TRUE                  ~ NA_character_
         )
  ) %>% 
  ggplot(aes(x = group,  y = value, color = group)) + 
  geom_boxplot() +  
  geom_jitter(alpha = .5) + 
  coord_flip() + 
  facet_wrap(~gene, ncol = 1)

Edit 2

library(ggplot2)
library(dplyr)
library(tidyr)
library(stringr)

marte <- tribble(
  ~gene, ~funnyName1, ~funnyName2, ~funnyName3, ~funnyName4, ~funnyName5, ~funnyName6,
  "AAA",  0.021383202,    0.016654469,    0.022484448,    0.025311535,    0.025495724,    0.02017925, 
  "TAG",  0.019927531,    0.018790672,    0.015649845,    0.02230479, 0.019363723,    0.02017925 ,
  "AGC",  0.013209711,    0.016891825,    0.014520044,    0.014302046,    0.014804269,    0.012904701 ,
  "TGT",  0.033757832,    0.034990209,    0.031899462,    0.034446096,    0.034475058,    0.031047513 ,
  "GAT",  0.013006661,    0.007615167,    0.009163947,    0.010540757,    0.008234933,    0.012000828 ,
  "CAC",  0.011210666,    0.015012758,    0.01241387, 0.011478221,    0.011045046,    0.013579884 ,
  "GGG",  0.012712095,    0.011927132,    0.013222864,    0.011558249,    0.014292494,    0.014647108 ,
  "CGA",  0.00230219, 0.000969203,    0.001325076,    0.002034983,    0.001656292,    0.002036438 ,
  "TCG",  0.004169681,    0.007377811,    0.005649008,    0.005133189,    0.006057561,    0.006131094 ,
  "ACA",  0.011259284,    0.013825979,    0.010656401,    0.009900537,    0.010617015,    0.009670358 ,
  "TTT",  0.033305974,    0.04751073, 0.043476442,    0.035212073,    0.037359611,    0.043669073 ,
  "ATC",  0.01259198, 0.013905097,    0.013222864,    0.013501772,    0.012087207,    0.010356431 ,
  "CCC",  0.009591983,    0.004213066,    0.006764862,    0.010506459,    0.006560031,    0.009354547 ,
  "GCT",  0.021391781,    0.025397077,    0.022972634,    0.024545558,    0.023513757,    0.024426367 ,
  "CTA",  0.012680636,    0.011848013,    0.013976065,    0.01610838, 0.014794964,    0.016128154 ,
  "GTG",  0.018394644,    0.015507249,    0.01591486, 0.01932091, 0.019856889,    0.017086478 ,
  "GGA",  0.017702557,    0.014182012,    0.018871872,    0.017926146,    0.018237817,    0.016411295 ,
  "CGG",  0.00377216, 0.00346144, 0.003361509,    0.00339545, 0.004029069,    0.004258007 ,
  "GAC",  0.019684443,    0.018790672,    0.025469356,    0.02854693, 0.027663791,    0.02270574 ,
  "CAT",  0.015297412,    0.014083114,    0.01355762, 0.013879044,    0.013771413,    0.01256711 ,
  "AGT",  0.018391784,    0.013054572,    0.012288337,    0.018532068,    0.014376239,    0.014745119 ,
  "TGC",  0.020382249,    0.025041043,    0.02170335, 0.02225906, 0.021708586,    0.02506888 ,
  "AAG",  0.016818859,    0.011393081,    0.018258153,    0.016920087,    0.016293071,    0.01251266 ,
  "TAA",  0.016710184,    0.019324723,    0.023697938,    0.021150109,    0.0213643,  0.019351607 ,
  "CTG",  0.034733046,    0.040864767,    0.036265238,    0.035143478,    0.036084824,    0.035555991 ,
  "GTA",  0.014556707,    0.012560081,    0.012706782,    0.014667886,    0.014320409,    0.013863025 ,
  "CCT",  0.015168718,    0.012184267,    0.012818367,    0.010735109,    0.012264002,    0.010988054 ,
  "GCC",  0.009183023,    0.007239354,    0.00776913, 0.007808391,    0.008197713,    0.007198319 ,
  "TTC",  0.018537637,    0.015922622,    0.018244205,    0.015639648,    0.017967972,    0.02003768 ,
  "ATT",  0.018097218,    0.017069842,    0.014743214,    0.015045158,    0.017204961,    0.017184488 ,
  "TCA",  0.015606277,    0.012757877,    0.013794739,    0.013936207,    0.011510296,    0.010323761 ,
  "ACG",  0.003929453,    0.002650474,    0.00380785, 0.003829885,    0.003535903,    0.003528374 ,
  "CCA",  0.013678729,    0.010601895,    0.016012498,    0.012964445,    0.014004038,    0.013340303 ,
  "GCG",  0.001401333,    0.000929644,    0.000864786,    0.00050303, 0.00042803, 0.000457382 ,
  "CTC",  0.021940875,    0.01946318, 0.021215164,    0.02198468, 0.022145921,    0.026560815 ,
  "GTT",  0.019249743,    0.023537789,    0.020141155,    0.020967189,    0.019614959,    0.020854433 ,
  "TCT",  0.032416556,    0.033704532,    0.033405864,    0.032696925,    0.034102858,    0.037919131 ,
  "ACC",  0.011316481,    0.013034792,    0.015133763,    0.011775466,    0.012384967,    0.013547214 ,
  "TTG",  0.029728284,    0.040330716,    0.03107652, 0.030993483,    0.031739385,    0.03275725 ,
  "ATA",  0.011276443,    0.010839251,    0.011395654,    0.008402881,    0.010635625,    0.013971925 ,
  "GAG",  0.011645365,    0.009454675,    0.007992301,    0.009397508,    0.008830453,    0.00750324 ,
  "CAA",  0.009388933,    0.007536048,    0.010935364,    0.008208529,    0.009658599,    0.009332767 ,
  "GGT",  0.010687311,    0.012738098,    0.00974977, 0.008711558,    0.01001219, 0.010977164 ,
  "CGC",  0.001201143,    0.001305457,    0.001325076,    0.001017492,    0.001079381,    0.001785967 ,
  "AAC",  0.013266908,    0.019146706,    0.015747482,    0.013193095,    0.014962454,    0.014418417 ,
  "TAT",  0.012557662,    0.011630437,    0.011814099,    0.011924088,    0.011435856,    0.011761247 ,
  "AGA",  0.019558609,    0.019502739,    0.017477055,    0.01982394, 0.017716737,    0.016160824 ,
  "TGG",  0.024234486,    0.028818957,    0.02414428, 0.024111124,    0.023439317,    0.024143226 ,
  "TTA",  0.015523341,    0.018493977,    0.01705861, 0.019572425,    0.016311681,    0.013111612 ,
  "ATG",  0.014385115,    0.006903099,    0.013153123,    0.013593232,    0.011742921,    0.012175068 ,
  "TCC",  0.014041931,    0.007872303,    0.00974977, 0.009671888,    0.009798174,    0.009909939 ,
  "ACT",  0.027183006,    0.030045295,    0.031020727,    0.034777638,    0.034130773,    0.033987825 ,
  "CTT",  0.02351094, 0.027256364,    0.026766536,    0.025631645,    0.02585862, 0.025656942 ,
  "GTC",  0.012952323,    0.012678759,    0.008745502,    0.008814451,    0.008076748,    0.00761214 ,
  "CCG",  0.002599616,    0.00114722, 0.002189862,    0.001783469,    0.002149457,    0.003081882 ,
  "GCA",  0.013684448,    0.02231145, 0.016486735,    0.016005488,    0.01599531, 0.018817995 ,
  "AGG",  0.014244982,    0.008722828,    0.013334449,    0.012381388,    0.012766472,    0.010770253 ,
  "TGA",  0.025881768,    0.019008248,    0.023098167,    0.023848177,    0.025532944,    0.023500713 ,
  "AAT",  0.016489975,    0.014538046,    0.018788183,    0.014004802,    0.018098242,    0.017881451 ,
  "TAC",  0.011036214,    0.00860415, 0.008271264,    0.008402881,    0.008635048,    0.011216745 ,
  "GGC",  0.01302668, 0.014142453,    0.011409602,    0.01280439, 0.011361416,    0.011576116 ,
  "CGT",  0.004718775,    0.006428388,    0.006346417,    0.004778781,    0.005378295,    0.00509654 ,
  "GAA",  0.020542402,    0.017841248,    0.018007086,    0.015102321,    0.018247122,    0.016171714 ,
  "CAG",  0.017162043,    0.018414858,    0.016472787,    0.016531382,    0.014981064,    0.014244177,
)
colnames(marte) <- c("gene", "a40", "b40", "c40", "a80", "b80", "c80")

marte %>% pivot_longer(-gene, names_to = "name") %>% 
  mutate(group = if_else(str_detect(name, "40"), "40s", "80s"),
         rep = case_when(
           str_detect(name, "a") ~ "rep1",
           str_detect(name, "b") ~ "rep2",
           str_detect(name, "c") ~ "rep3", 
           TRUE                  ~ NA_character_
         )
  ) %>% 
  ggplot(aes(x = group,  y = value, color = group)) + 
  geom_boxplot() +  
  geom_jitter(alpha = .5) + 
  coord_flip() + 
  facet_wrap(~gene, ncol = 4)

^{Created on 2021-07-09 by the reprex package (v2.0.0)}

Okay it's starting to come together. I want to have for each trinucleotide(gene) 3 pairs of boxes so 1 pair for 40s and 80s rep1, 1 pair for 40s and 80s rep2 and 1 pair for 40s and 80s rep3. "Rep" is short for replicate so there are 3 replicates — user14687500, Jul 01 '21 at 13:34
But will there be still variation for each gene after the ungrouping? In the dataset in the pastebin each gene comes up only once (with 6 unique values across each group [40,80] and each rep [a,b,c]). Unless your data is bigger than you pasted, there will be only one single point left for each gene. Right? [note that I updated my answer to account for the replications now... is it still not what you were looking for?] — Marcelo Avila, Jul 01 '21 at 13:39
Are you able to access this: https://i.stack.imgur.com/cL4YB.jpg — user14687500, Jul 01 '21 at 14:07
yes, i did. But for me it is not clear what the differences are, apart from cosmetic ones. I am not able to reproduce a graph very similar to your a draft. But if you point out exactly what you expected to be different (and specially if it is not only a thematic/cosmetic difference) I can try to improve my answer :) — Marcelo Avila, Jul 06 '21 at 11:34
I am just having an issue when I try to plot all of the 64 trinucleotides. The code is only showing 10 and some are just lines and not box plots. I have edited the question with the code I used — user14687500, Jul 07 '21 at 16:19
And I was hoping to combine rep1,2and3 for each group so that I only have 2 boxed (1 red 1 blue) — user14687500, Jul 07 '21 at 21:09
you only have a vertical line instead of box-plots for some groups because there is only one observation for that group, right? You can add ` geom_point() + ` in the ggplot call so you can see each point. — Marcelo Avila, Jul 07 '21 at 21:25
Yes! It looks great. Is there a reason why it won't plot all 64 nucleotides? — user14687500, Jul 08 '21 at 19:03
See my last edit. Your tibble was returning a error because you need to quote strings (AAA -> "AAA"). With all nucleotides, the plot might get a bit crowded. You may consider filtering out a few nucleotides at a time and creating multiple plots, such as `filter(gene %in% c("AAA", "TAG", "AGC", "TGT")) %>%` right before calling ggplot — Marcelo Avila, Jul 09 '21 at 10:07
Hello Marcelo. I am not sure if you still have some time to look into this but I need to take the average of the 3 replicates for 40s and for 80s and plot that as the value. Do you have any suggestions on how to do that? — user14687500, Jul 14 '21 at 13:33
adding `stat_summary(fun = ~ mean(.x), geom = "point", shape = 2, size = 4, color = "black") +` after geom_boxplot() could do it... it depends exactly how you want to group the variables. Other option would be grouping by the desired variables and generating (with `mutate()`) the average value. — Marcelo Avila, Jul 14 '21 at 14:32
I might not have been very clear. I edited my question to include the "average". It's under the column control. I want it as a black box on each of the trinucleotide such that each trinucleotide has 3 boxes. — user14687500, Jul 14 '21 at 19:56
it would not be a box plot, then, right? because it is going to be only one observation for the average group. (Or do the trinucleotide repeat down the data set?) . I would suggest you write a new question, other people might chime in as well... — Marcelo Avila, Jul 16 '21 at 19:29

Plotting a box plot from a table with 7 columns

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