GO enrichment
Philipp Bayer
01/10/2021
Last updated: 2022-02-28
Checks: 7 0
Knit directory: Amphibolis_Posidonia_Comparison/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 581bebd | Philipp Bayer | 2022-02-28 | accidentally did not display REVIGO code |
| html | 6eeb3ed | Philipp Bayer | 2022-02-25 | Add missing files |
| html | 9ca6c94 | Philipp Bayer | 2022-02-25 | Build site. |
| Rmd | 61c8f69 | Philipp Bayer | 2022-02-25 | Replace GO enrichment |
| html | 9b59467 | Philipp Bayer | 2022-02-23 | Rewrite Orthofinder analysis |
| Rmd | ab9a1f6 | Philipp Bayer | 2022-02-21 | add some more changes |
| html | 65d3fa4 | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 21f4c6f | Philipp Bayer | 2021-12-20 | fix tables again, finally :) haha |
| html | d8ec8d3 | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 2fb63eb | Philipp Bayer | 2021-12-20 | fix tables again, finally :) |
| html | cf2e045 | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 280fc5d | Philipp Bayer | 2021-12-20 | fix tables again |
| html | 5356e2c | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 9f4be6f | Philipp Bayer | 2021-12-20 | fix tables |
| html | 7816b8c | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 73bffa4 | Philipp Bayer | 2021-12-20 | add tables |
| html | c1288a4 | Philipp Bayer | 2021-12-20 | Build site. |
| Rmd | 2691cad | Philipp Bayer | 2021-12-20 | add tables |
| html | 292db59 | Philipp Bayer | 2021-10-18 | Build site. |
| Rmd | 35aa72f | Philipp Bayer | 2021-10-18 | wflow_publish(c(“analysis/GOenrichment.Rmd”, “analysis/plotGenes.Rmd”, |
| Rmd | 7e370e9 | Philipp Bayer | 2021-10-07 | Updated GOenrichment |
| Rmd | 95586f9 | Philipp Bayer | 2021-10-07 | Add missing data |
| html | 95586f9 | Philipp Bayer | 2021-10-07 | Add missing data |
| html | c0db4a5 | Philipp Bayer | 2021-10-07 | Build site. |
| Rmd | 08b28ea | Philipp Bayer | 2021-10-07 | wflow_publish(files = c("analysis/*")) |
Lost in seagrasses
The GO enrichment does not work well on my laptop so I’m setting this to eval=FALSE and run it on a remote server. The script which writes the input files is a Python script in the scripts/ folder: findClustersUniqueToAquatic.py. This script parses Orthofinder output to pull out genome-specific groups and genes.
# give properly formatted background in format: GO:0005838 GSBRNA2T00088508001;GSBRNA2T00088313001;GSBRNA2T00035842001
#annAT <- readMappings('BACKGROUND.txt.gz', sep="\t", IDsep=";")
#save(annAT, file='annAtObject.RData')
load('annAtObject.RData')
allgenes <- unique(unlist(annAT))
compare <- function(genelistfile, outname, allgenes, annAT) {
# give file with your genes of interest, one gene_id per line
mygenes <-scan(genelistfile ,what="")
geneList <- factor(as.integer(allgenes %in% mygenes))
names(geneList) <- allgenes
GOdata <-new ("topGOdata", ontology = 'BP', allGenes = geneList, nodeSize = 5, annot=annFUN.GO2genes, GO2genes=annAT)
# using ClassicCount:
#test.stat <-new ("classicCount", testStatistic = GOFisherTest, name = "Fisher Test")
#resultsFisherC <-getSigGroups (GOdata, test.stat)
# using weight01:
weight01.fisher <- runTest(GOdata, statistic = "fisher")
# using ClassicCount:
# allRes <- GenTable(GOdata, classicFisher= resultsFisherC, topNodes = 30)
# using weight01:
allRes <- GenTable(GOdata, classicFisher=weight01.fisher,topNodes=30)#,topNodes=100)
names(allRes)[length(allRes)] <- "p.value"
p_values <- score(weight01.fisher)
adjusted_p <- p.adjust(p_values)
adjusted_p[adjusted_p < 0.05] %>% enframe() %>% write_csv('data/' + outname)
}Comparing the three big groups
# all genes shared - this runs out of memory
#compare('Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses_and_Terrestrials.txt', 'output/GO_results_genes_in_Aquatics_and_Seagrasses_and_Terrestrials.csv', allgenes, annAT)
# Genes in aquatics and seagrasses - IMPORTANT This is NOT the union - this is the intersection!
# Union is below
compare('Lost_present_gene_lists/Genes_only_in_Aquatics_and_Seagrasses.txt', 'output/GO_results_genes_in_Aquatics_and_Seagrasses_NOT_Terrestrials.csv', allgenes, annAT)
# Genes only in aquatics
compare('Lost_present_gene_lists/Genes_only_in_Aquatics.txt', 'output/GO_results_genes_in_Aquatics_NOT_Seagrasses_NOT_Terrestrials.csv', allgenes, annAT)
# Genes only in seagrasses
compare('Lost_present_gene_lists/Genes_only_in_Seagrasses.txt', 'output/GO_results_genes_in_Seagrasses_NOT_Aquatics_NOT_Terrestrials.csv', allgenes, annAT)
# Genes only in terrestrials
compare('Lost_present_gene_lists/Genes_only_in_Terrestrials.txt', 'output/GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv', allgenes, annAT)
# Genes union of Seagrass and Aquatics
compare('Lost_present_gene_lists/Genes_union_of_Seagrass_and_Aquatics_union.txt', 'output/GO_results_genes_union_Aquatics_and_Seagrasses_NOT_Terrestrials.csv', allgenes, annAT)Seagrass only comparisons
Now we compare seagrasses within each other.
For the seagrass-only comparisons, I’m using a Seagrass-only background as that makes more biological sense to me.s
# give properly formatted background in format: GO:0005838 GSBRNA2T00088508001;GSBRNA2T00088313001;GSBRNA2T00035842001
#sannAT <- readMappings('SEAGRASSBACKGROUND.txt', sep="\t", IDsep=";")
#save(sannAT, file='sannAtObject.RData')
load('sannAtObject.RData')
sallgenes <- unique(unlist(sannAT))lost in seagrasses
compare('Lost_present_gene_lists/Genes_lost_in_A_antarctica_not_other_seagrasses.txt', 'output/GO_results_genes_lost_A_antarctica_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_lost_in_Z_marina_not_other_seagrasses.txt', 'output/GO_results_genes_lost_Z_marina_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_lost_in_P_australis_not_other_seagrasses.txt', 'output/GO_results_genes_lost_P_australis_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_lost_in_Z_muelleri_not_other_seagrasses.txt', 'output/GO_results_genes_lost_Z_muelleri_not_other_seagrasses.csv', sallgenes, sannAT)Present in seagrasses
compare('Lost_present_gene_lists/Genes_only_in_Z_marina_not_other_seagrasses.txt', 'output/GO_results_genes_only_Z_marina_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_only_in_Z_muelleri_not_other_seagrasses.txt', 'output/GO_results_genes_only_Z_muelleri_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_only_in_P_australis_not_other_seagrasses.txt', 'output/GO_results_genes_only_P_australis_not_other_seagrasses.csv', sallgenes, sannAT)
compare('Lost_present_gene_lists/Genes_only_in_A_antarctica_not_other_seagrasses.txt', 'output/GO_results_genes_only_A_antarctica_not_other_seagrasses.csv', sallgenes, sannAT)Alright now we have all these different GO terms in all these files - we can send them to revigo for visualiation and some deduplication!
Revigo
This code is based on http://revigo.irb.hr/CodeExamples/revigo.R.txt
results_list <- list()
for (f in list.files('./output/', pattern='*.csv')){
filename <- paste('./output/', f, sep='')
go_and_pvalues <- readChar(filename, file.info(filename)$size)
go_and_pvalues <- gsub(',', ' ', go_and_pvalues)
httr::POST(
url = "http://revigo.irb.hr/StartJob.aspx",
body = list(
cutoff = "0.7",
valueType = "pvalue",
# speciesTaxon = "4577", # zea mays
#speciesTaxon = '39947', # japonica
speciesTaxon = '3702', # arabidopsis
measure = "SIMREL",
goList = go_and_pvalues
),
# application/x-www-form-urlencoded
encode = "form"
) -> res
dat <- httr::content(res, encoding = "UTF-8")
jobid <- jsonlite::fromJSON(dat,bigint_as_char=TRUE)$jobid
# Check job status
running <- "1"
while (running != "0" ) {
httr::POST(
url = "http://revigo.irb.hr/QueryJobStatus.aspx",
query = list( jobid = jobid )
) -> res2
dat2 <- httr::content(res2, encoding = "UTF-8")
running <- jsonlite::fromJSON(dat2)$running
Sys.sleep(1)
}
# Fetch results
httr::POST(
url = "http://revigo.irb.hr/ExportJob.aspx",
query = list(
jobid = jobid,
namespace = "1",
type = "CSVTable"
)
) -> res3
dat3 <- httr::content(res3, encoding = "UTF-8")
dat3 <- stri_replace_all_fixed(dat3, "\r", "")
# Now we have a csv table in a string!
# read_csv does not like the ', ', it wants ','
dat <- read_csv(gsub(', ', ',', dat3), show_col_types = FALSE)
# do we even have results?
if(nrow(dat) == 0){next}
results_list[[f]] <- dat
}Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nuls
Warning in readChar(filename, file.info(filename)$size): truncating string with
embedded nulsOK we have a list with all results in a big list. Now we can plot!
# lots of warnings and messages here so I'm hiding these
plot_list <- list()
for (f in names(results_list)) {
dat <- results_list[[f]]
if(nrow(dat) == 0) {next}
names(dat) <- c("term_ID","description","frequency", 'plot_X', 'plot_Y', 'log_size', 'value', 'uniqueness', 'dispensability', 'eliminated', 'representative')
one.data <- dat
if (one.data[1,] == '<html>') {next} # some datasets result in error
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null") & (! is.na(one.data$frequency)) & (one.data$value != 'null'), ];
one.data <- suppressMessages(type_convert(one.data)) # guess data types, but also: shush
top_ten_values <- one.data %>% arrange(value) %>% head(10) %>% pull(term_ID)
one.data <- one.data %>% mutate(description2 = case_when(
term_ID %in% top_ten_values ~ description,
TRUE ~ ''))
p1 <-
ggplot(data = one.data, aes(plot_X, plot_Y, label = description2)) +
geom_point(aes(colour = value, size = log_size), alpha = I(0.6)) +
scale_size_area() +
scale_colour_gradientn(colours = rev(wes_palette("Zissou1", 100, type = "continuous")),
limits = c(min(one.data$value), 0)) +
geom_point(
aes(plot_X, plot_Y, size = log_size),
shape = 21,
fill = "transparent",
colour = I (alpha ("black", 0.6))
) +
scale_size_area() +
geom_label_repel(max.overlaps = Inf, box.padding = 0.5,
aes(point.size = log_size), alpha=0.9) +
theme_minimal() +
labs(color = 'log(p-value)',
size = 'Frequency') +
theme(
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
NULL
#ggtitle(f)
plot_list[[f]] <- p1
}Making Supplementary Tables for the REVIGO results
Let’s also pull these terms out as tables. Value is the unadjusted p-value (-3.7 = 10 * -3.7)
for( i in names(results_list)) {
print(i)
print(results_list[[i]] %>% filter(Eliminated == FALSE) %>% select(TermID, Name, Value) %>% arrange(Value) %>% kbl() %>% kable_styling())
cat("\n")
}| TermID | Name | Value |
|---|---|---|
| GO:0032197 | transposition,RNA-mediated | -67.507734 |
| GO:0006278 | RNA-dependent DNA biosynthetic process | -49.118091 |
| GO:0090501 | RNA phosphodiester bond hydrolysis | -43.436290 |
| GO:0006508 | proteolysis | -28.556828 |
| GO:0045747 | positive regulation of Notch signaling pathway | -21.348070 |
| GO:0016360 | sensory organ precursor cell fate determination | -21.348070 |
| GO:0045314 | regulation of compound eye photoreceptor development | -21.348070 |
| GO:0007398 | ectoderm development | -21.348070 |
| GO:0035204 | negative regulation of lamellocyte differentiation | -21.348070 |
| GO:2000027 | regulation of animal organ morphogenesis | -21.236806 |
| GO:0007616 | long-term memory | -21.231089 |
| GO:0030718 | germ-line stem cell population maintenance | -18.709600 |
| GO:0007422 | peripheral nervous system development | -18.628472 |
| GO:0007498 | mesoderm development | -18.628472 |
| GO:0030707 | ovarian follicle cell development | -17.937024 |
| GO:0033962 | P-body assembly | -12.505301 |
| GO:0000290 | deadenylation-dependent decapping of nuclear-transcribed mRNA | -10.390740 |
| GO:0008104 | protein localization | -8.899044 |
| GO:0001896 | autolysis | -8.396837 |
| GO:0043386 | mycotoxin biosynthetic process | -8.396837 |
| GO:0010914 | positive regulation of sterigmatocystin biosynthetic process | -8.396837 |
| GO:0051260 | protein homooligomerization | -7.067176 |
| GO:0008356 | asymmetric cell division | -6.018134 |
| GO:0000209 | protein polyubiquitination | -5.141380 |
| GO:0010501 | RNA secondary structure unwinding | -5.076995 |
| GO:0009062 | fatty acid catabolic process | -4.163845 |
| GO:0042306 | regulation of protein import into nucleus | -3.362772 |
| GO:0016446 | somatic hypermutation of immunoglobulin genes | -3.103944 |
| GO:0010098 | suspensor development | -2.948600 |
| GO:0040007 | growth | -2.774732 |
| GO:0097164 | ammonium ion metabolic process | -2.588258 |
| GO:0019365 | pyridine nucleotide salvage | -2.389379 |
| GO:0006657 | CDP-choline pathway | -2.045139 |
| GO:0006458 | ‘de novo’ protein folding | -2.026123 |
| GO:0016560 | protein import into peroxisome matrix,docking | -1.985661 |
| GO:0098719 | sodium ion import across plasma membrane | -1.614660 |
| GO:1904580 | regulation of intracellular mRNA localization | -1.534859 |
| GO:0006970 | response to osmotic stress | -1.532272 |
| GO:0046520 | sphingoid biosynthetic process | -1.482379 |
| GO:0010555 | response to mannitol | -1.441326 |
| GO:0006885 | regulation of pH | -1.341458 |
| TermID | Name | Value |
|---|---|---|
| GO:0010025 | wax biosynthetic process | -26.626443 |
| GO:0019432 | triglyceride biosynthetic process | -25.954024 |
| GO:0048438 | floral whorl development | -25.054223 |
| GO:0009753 | response to jasmonic acid | -13.955898 |
| GO:0017148 | negative regulation of translation | -13.764822 |
| GO:2000117 | negative regulation of cysteine-type endopeptidase activity | -12.436518 |
| GO:0006869 | lipid transport | -10.654295 |
| GO:0009723 | response to ethylene | -10.158676 |
| GO:0090696 | post-embryonic plant organ development | -9.654049 |
| GO:0001666 | response to hypoxia | -9.070723 |
| GO:0001101 | response to acid chemical | -8.606000 |
| GO:0034605 | cellular response to heat | -8.228346 |
| GO:0010373 | negative regulation of gibberellin biosynthetic process | -7.331038 |
| GO:0010208 | pollen wall assembly | -6.453670 |
| GO:0009266 | response to temperature stimulus | -6.229266 |
| GO:0010030 | positive regulation of seed germination | -6.157498 |
| GO:0006606 | protein import into nucleus | -5.868931 |
| GO:0019365 | pyridine nucleotide salvage | -5.687459 |
| GO:0042254 | ribosome biogenesis | -5.646111 |
| GO:0010220 | positive regulation of vernalization response | -5.563470 |
| GO:0006355 | regulation of transcription,DNA-templated | -4.209775 |
| GO:0009910 | negative regulation of flower development | -3.634419 |
| GO:0048441 | petal development | -3.509074 |
| GO:0006396 | RNA processing | -3.319062 |
| GO:0090143 | nucleoid organization | -3.064675 |
| GO:0009416 | response to light stimulus | -2.859747 |
| GO:0010262 | somatic embryogenesis | -2.802825 |
| GO:0032353 | negative regulation of hormone biosynthetic process | -2.781174 |
| GO:0050821 | protein stabilization | -2.655356 |
| GO:0009650 | UV protection | -2.631031 |
| GO:0006212 | uracil catabolic process | -2.393548 |
| GO:0009093 | cysteine catabolic process | -2.271820 |
| GO:0048830 | adventitious root development | -2.256427 |
| GO:0009739 | response to gibberellin | -1.992537 |
| GO:0042814 | monopolar cell growth | -1.754299 |
| GO:0072699 | protein localization to cortical microtubule cytoskeleton | -1.754299 |
| GO:0085029 | extracellular matrix assembly | -1.708512 |
| GO:0010077 | maintenance of inflorescence meristem identity | -1.620899 |
| GO:0055046 | microgametogenesis | -1.407736 |
| TermID | Name | Value |
|---|---|---|
| GO:0051603 | proteolysis involved in cellular protein catabolic process | -11.456833 |
| GO:0006278 | RNA-dependent DNA biosynthetic process | -9.577934 |
| GO:0032197 | transposition,RNA-mediated | -9.168511 |
| GO:0033275 | actin-myosin filament sliding | -6.682353 |
| GO:0090501 | RNA phosphodiester bond hydrolysis | -6.648430 |
| GO:0043007 | maintenance of rDNA | -6.455202 |
| GO:0033298 | contractile vacuole organization | -5.583611 |
| GO:0032060 | bleb assembly | -5.583611 |
| GO:0050982 | detection of mechanical stimulus | -5.431629 |
| GO:1900049 | regulation of histone exchange | -5.042366 |
| GO:0016131 | brassinosteroid metabolic process | -4.909247 |
| GO:1902466 | positive regulation of histone H3-K27 trimethylation | -4.579819 |
| GO:0051591 | response to cAMP | -4.509703 |
| GO:0001932 | regulation of protein phosphorylation | -3.934885 |
| GO:0032989 | cellular component morphogenesis | -3.724531 |
| GO:0048578 | positive regulation of long-day photoperiodism,flowering | -3.385409 |
| GO:0006468 | protein phosphorylation | -3.226314 |
| GO:0080156 | mitochondrial mRNA modification | -3.221374 |
| GO:0097193 | intrinsic apoptotic signaling pathway | -3.003236 |
| GO:0009048 | dosage compensation by inactivation of X chromosome | -2.792735 |
| GO:0090701 | specification of plant organ identity | -2.713400 |
| GO:0010022 | meristem determinacy | -2.675579 |
| GO:0006971 | hypotonic response | -2.372108 |
| GO:0010090 | trichome morphogenesis | -2.336224 |
| GO:0051707 | response to other organism | -2.284036 |
| GO:0051555 | flavonol biosynthetic process | -2.102840 |
| GO:1904872 | regulation of telomerase RNA localization to Cajal body | -1.978326 |
| GO:0051127 | positive regulation of actin nucleation | -1.905381 |
| GO:0097242 | amyloid-beta clearance | -1.718349 |
| GO:0010992 | ubiquitin recycling | -1.718349 |
| GO:0010815 | bradykinin catabolic process | -1.718349 |
| GO:2001240 | negative regulation of extrinsic apoptotic signaling pathway in absence of ligand | -1.641177 |
| GO:0016926 | protein desumoylation | -1.543029 |
| GO:0071048 | nuclear retention of unspliced pre-mRNA at the site of transcription | -1.532452 |
| GO:0010222 | stem vascular tissue pattern formation | -1.487551 |
| GO:0010492 | maintenance of shoot apical meristem identity | -1.433920 |
| GO:0048576 | positive regulation of short-day photoperiodism,flowering | -1.364131 |
| GO:0043086 | negative regulation of catalytic activity | -1.351735 |
| GO:0031154 | culmination involved in sorocarp development | -1.309504 |
| TermID | Name | Value |
|---|---|---|
| GO:0051762 | sesquiterpene biosynthetic process | -143.501548 |
| GO:0006952 | defense response | -117.942439 |
| GO:0010082 | regulation of root meristem growth | -108.551199 |
| GO:2000280 | regulation of root development | -86.448127 |
| GO:0007165 | signal transduction | -73.886537 |
| GO:0046345 | abscisic acid catabolic process | -57.837256 |
| GO:0000966 | RNA 5’-end processing | -56.420803 |
| GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | -52.213782 |
| GO:0048509 | regulation of meristem development | -51.881994 |
| GO:0045338 | farnesyl diphosphate metabolic process | -41.706252 |
| GO:2000026 | regulation of multicellular organismal development | -40.141627 |
| GO:0051554 | flavonol metabolic process | -37.734717 |
| GO:0009819 | drought recovery | -36.208841 |
| GO:0010469 | regulation of signaling receptor activity | -36.089822 |
| GO:0090615 | mitochondrial mRNA processing | -35.930259 |
| GO:0019756 | cyanogenic glycoside biosynthetic process | -35.084917 |
| GO:0080003 | thalianol metabolic process | -31.306539 |
| GO:0009617 | response to bacterium | -31.074845 |
| GO:0009625 | response to insect | -29.065755 |
| GO:0009962 | regulation of flavonoid biosynthetic process | -26.749126 |
| GO:0006468 | protein phosphorylation | -26.047386 |
| GO:0006885 | regulation of pH | -23.177460 |
| GO:0016567 | protein ubiquitination | -23.062311 |
| GO:0010618 | aerenchyma formation | -21.148233 |
| GO:0045168 | cell-cell signaling involved in cell fate commitment | -21.038631 |
| GO:0052544 | defense response by callose deposition in cell wall | -19.928674 |
| GO:2000083 | negative regulation of L-ascorbic acid biosynthetic process | -19.592316 |
| GO:0000304 | response to singlet oxygen | -18.701819 |
| GO:0071368 | cellular response to cytokinin stimulus | -17.533700 |
| GO:0045926 | negative regulation of growth | -16.846454 |
| GO:1902025 | nitrate import | -16.819160 |
| GO:0060307 | regulation of ventricular cardiac muscle cell membrane repolarization | -16.402211 |
| GO:0036371 | protein localization to T-tubule | -16.095554 |
| GO:0033292 | T-tubule organization | -16.095554 |
| GO:0036309 | protein localization to M-band | -16.095554 |
| GO:1901021 | positive regulation of calcium ion transmembrane transporter activity | -16.095554 |
| GO:0009626 | plant-type hypersensitive response | -15.316450 |
| GO:0097185 | cellular response to azide | -14.492924 |
| GO:0080027 | response to herbivore | -14.021250 |
| GO:0010221 | negative regulation of vernalization response | -13.971217 |
| GO:0042742 | defense response to bacterium | -13.848529 |
| GO:0080184 | response to phenylpropanoid | -13.215717 |
| GO:0009684 | indoleacetic acid biosynthetic process | -12.791295 |
| GO:0009871 | jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway | -12.418186 |
| GO:0071236 | cellular response to antibiotic | -11.827987 |
| GO:0009852 | auxin catabolic process | -11.760676 |
| GO:0010942 | positive regulation of cell death | -11.630087 |
| GO:0071466 | cellular response to xenobiotic stimulus | -11.288199 |
| GO:0071766 | Actinobacterium-type cell wall biogenesis | -10.455440 |
| GO:0007166 | cell surface receptor signaling pathway | -10.403838 |
| GO:1904526 | regulation of microtubule binding | -10.390529 |
| GO:0009611 | response to wounding | -10.241320 |
| GO:0009410 | response to xenobiotic stimulus | -9.812383 |
| GO:0006812 | cation transport | -9.518886 |
| GO:1905255 | regulation of RNA binding transcription factor activity | -9.396917 |
| GO:0035024 | negative regulation of Rho protein signal transduction | -8.998029 |
| GO:0009914 | hormone transport | -8.966261 |
| GO:0010930 | negative regulation of auxin mediated signaling pathway | -8.845442 |
| GO:0002213 | defense response to insect | -8.830445 |
| GO:0071395 | cellular response to jasmonic acid stimulus | -8.620748 |
| GO:0070301 | cellular response to hydrogen peroxide | -8.478385 |
| GO:0002011 | morphogenesis of an epithelial sheet | -8.038068 |
| GO:0010030 | positive regulation of seed germination | -8.035314 |
| GO:0016045 | detection of bacterium | -7.948233 |
| GO:0097237 | cellular response to toxic substance | -7.664251 |
| GO:1902265 | abscisic acid homeostasis | -7.523139 |
| GO:0034394 | protein localization to cell surface | -6.648005 |
| GO:0009865 | pollen tube adhesion | -6.357568 |
| GO:0006355 | regulation of transcription,DNA-templated | -6.326918 |
| GO:0090559 | regulation of membrane permeability | -6.145108 |
| GO:0007584 | response to nutrient | -6.032889 |
| GO:0009866 | induced systemic resistance,ethylene mediated signaling pathway | -6.031631 |
| GO:0010310 | regulation of hydrogen peroxide metabolic process | -5.857372 |
| GO:0097167 | circadian regulation of translation | -5.774298 |
| GO:0009734 | auxin-activated signaling pathway | -5.408543 |
| GO:0003283 | atrial septum development | -5.371665 |
| GO:0007267 | cell-cell signaling | -5.269003 |
| GO:0009737 | response to abscisic acid | -5.143354 |
| GO:0009311 | oligosaccharide metabolic process | -5.050193 |
| GO:0010233 | phloem transport | -5.045523 |
| GO:0009826 | unidimensional cell growth | -4.938939 |
| GO:0010114 | response to red light | -4.892294 |
| GO:0071218 | cellular response to misfolded protein | -4.859071 |
| GO:0061157 | mRNA destabilization | -4.507855 |
| GO:0010438 | cellular response to sulfur starvation | -4.191383 |
| GO:0007422 | peripheral nervous system development | -4.020084 |
| GO:0031542 | positive regulation of anthocyanin biosynthetic process | -3.961486 |
| GO:0002239 | response to oomycetes | -3.957108 |
| GO:0015708 | silicic acid import across plasma membrane | -3.932028 |
| GO:0006335 | DNA replication-dependent chromatin assembly | -3.844884 |
| GO:0032504 | multicellular organism reproduction | -3.826316 |
| GO:0009745 | sucrose mediated signaling | -3.815288 |
| GO:0035600 | tRNA methylthiolation | -3.689252 |
| GO:0001101 | response to acid chemical | -3.608320 |
| GO:0009751 | response to salicylic acid | -3.586672 |
| GO:1905614 | negative regulation of developmental vegetative growth | -3.393833 |
| GO:0032527 | protein exit from endoplasmic reticulum | -3.369785 |
| GO:0010305 | leaf vascular tissue pattern formation | -3.344485 |
| GO:1902290 | positive regulation of defense response to oomycetes | -3.258939 |
| GO:0051513 | regulation of monopolar cell growth | -3.182886 |
| GO:0002230 | positive regulation of defense response to virus by host | -3.125303 |
| GO:0097503 | sialylation | -3.117517 |
| GO:0006898 | receptor-mediated endocytosis | -3.067736 |
| GO:0009960 | endosperm development | -2.946166 |
| GO:0043086 | negative regulation of catalytic activity | -2.893705 |
| GO:0009733 | response to auxin | -2.892061 |
| GO:0031347 | regulation of defense response | -2.842056 |
| GO:0042177 | negative regulation of protein catabolic process | -2.756067 |
| GO:0045314 | regulation of compound eye photoreceptor development | -2.705864 |
| GO:0007398 | ectoderm development | -2.705864 |
| GO:0045747 | positive regulation of Notch signaling pathway | -2.705864 |
| GO:0035204 | negative regulation of lamellocyte differentiation | -2.705864 |
| GO:0010150 | leaf senescence | -2.704461 |
| GO:0071229 | cellular response to acid chemical | -2.695489 |
| GO:0031640 | killing of cells of other organism | -2.629273 |
| GO:1903553 | positive regulation of extracellular exosome assembly | -2.629137 |
| GO:0044364 | disruption of cells of other organism | -2.629137 |
| GO:0048265 | response to pain | -2.629137 |
| GO:2000027 | regulation of animal organ morphogenesis | -2.615330 |
| GO:0007498 | mesoderm development | -2.610391 |
| GO:0048821 | erythrocyte development | -2.525503 |
| GO:1905663 | positive regulation of telomerase RNA reverse transcriptase activity | -2.437567 |
| GO:0009627 | systemic acquired resistance | -2.272801 |
| GO:0009828 | plant-type cell wall loosening | -2.257521 |
| GO:0010275 | NAD(P)H dehydrogenase complex assembly | -2.187116 |
| GO:1904355 | positive regulation of telomere capping | -1.975465 |
| GO:1900745 | positive regulation of p38MAPK cascade | -1.870783 |
| GO:0031930 | mitochondria-nucleus signaling pathway | -1.675324 |
| GO:0046482 | para-aminobenzoic acid metabolic process | -1.654849 |
| GO:0001824 | blastocyst development | -1.628424 |
| GO:0071219 | cellular response to molecule of bacterial origin | -1.522636 |
| GO:0097366 | response to bronchodilator | -1.511918 |
| GO:0002215 | defense response to nematode | -1.438176 |
| GO:0042761 | very long-chain fatty acid biosynthetic process | -1.415808 |
| GO:0009958 | positive gravitropism | -1.402316 |
| GO:0000769 | syncytium formation by mitosis without cytokinesis | -1.356437 |
| GO:0045056 | transcytosis | -1.355560 |
| GO:0048211 | Golgi vesicle docking | -1.355560 |
| GO:0032526 | response to retinoic acid | -1.346440 |
| GO:0009218 | pyrimidine ribonucleotide metabolic process | -1.324744 |
| GO:0090548 | response to nitrate starvation | -1.315645 |
| GO:0006424 | glutamyl-tRNA aminoacylation | -1.313120 |
| TermID | Name | Value |
|---|---|---|
| GO:0006278 | RNA-dependent DNA biosynthetic process | -180.916060 |
| GO:0032197 | transposition,RNA-mediated | -175.316613 |
| GO:0090501 | RNA phosphodiester bond hydrolysis | -160.989575 |
| GO:0006508 | proteolysis | -72.416255 |
| GO:0090305 | nucleic acid phosphodiester bond hydrolysis | -55.006996 |
| GO:0009451 | RNA modification | -51.871677 |
| GO:0044550 | secondary metabolite biosynthetic process | -23.892755 |
| GO:0010726 | positive regulation of hydrogen peroxide metabolic process | -18.244993 |
| GO:0080181 | lateral root branching | -14.606194 |
| GO:0032350 | regulation of hormone metabolic process | -11.320614 |
| GO:0051258 | protein polymerization | -10.767659 |
| GO:0071395 | cellular response to jasmonic acid stimulus | -10.138487 |
| GO:0016101 | diterpenoid metabolic process | -9.758264 |
| GO:0010942 | positive regulation of cell death | -9.704042 |
| GO:0044245 | polysaccharide digestion | -6.692450 |
| GO:0016081 | synaptic vesicle docking | -6.692450 |
| GO:0032260 | response to jasmonic acid stimulus involved in jasmonic acid and ethylene-dependent systemic resistance | -6.439823 |
| GO:0051603 | proteolysis involved in cellular protein catabolic process | -6.039701 |
| GO:0015695 | organic cation transport | -5.617644 |
| GO:0048462 | carpel formation | -4.934992 |
| GO:0010337 | regulation of salicylic acid metabolic process | -4.452476 |
| GO:0072488 | ammonium transmembrane transport | -4.131855 |
| GO:0045962 | positive regulation of development,heterochronic | -4.056345 |
| GO:0040007 | growth | -3.522516 |
| GO:1900049 | regulation of histone exchange | -3.227057 |
| GO:0071289 | cellular response to nickel ion | -3.177715 |
| GO:0015709 | thiosulfate transport | -3.177715 |
| GO:0033259 | plastid DNA replication | -3.177715 |
| GO:0006182 | cGMP biosynthetic process | -2.777287 |
| GO:0006032 | chitin catabolic process | -2.777287 |
| GO:0007165 | signal transduction | -2.454269 |
| GO:0009629 | response to gravity | -2.417378 |
| GO:0009694 | jasmonic acid metabolic process | -2.381020 |
| GO:0043086 | negative regulation of catalytic activity | -2.306902 |
| GO:0080021 | response to benzoic acid | -2.299520 |
| GO:0072756 | cellular response to paraquat | -2.299520 |
| GO:0071465 | cellular response to desiccation | -2.299520 |
| GO:0034265 | isopentenyl adenine biosynthetic process | -2.299520 |
| GO:0070562 | regulation of vitamin D receptor signaling pathway | -2.278555 |
| GO:0048385 | regulation of retinoic acid receptor signaling pathway | -2.278555 |
| GO:0002229 | defense response to oomycetes | -2.187161 |
| GO:0006012 | galactose metabolic process | -2.057857 |
| GO:0010258 | NADH dehydrogenase complex (plastoquinone) assembly | -1.880093 |
| GO:0051707 | response to other organism | -1.559465 |
| GO:0034461 | uropod retraction | -1.484321 |
| GO:0090284 | positive regulation of protein glycosylation in Golgi | -1.465553 |
| GO:0042773 | ATP synthesis coupled electron transport | -1.424052 |
| GO:0080143 | regulation of amino acid export | -1.421822 |
| GO:0043153 | entrainment of circadian clock by photoperiod | -1.421822 |
| GO:0015990 | electron transport coupled proton transport | -1.421822 |
| GO:0008347 | glial cell migration | -1.366082 |
| TermID | Name | Value |
|---|---|---|
| GO:0009451 | RNA modification | -89.911120 |
| GO:0090305 | nucleic acid phosphodiester bond hydrolysis | -89.381091 |
| GO:0006278 | RNA-dependent DNA biosynthetic process | -20.038600 |
| GO:0032197 | transposition,RNA-mediated | -19.701475 |
| GO:0090501 | RNA phosphodiester bond hydrolysis | -17.299422 |
| GO:0051603 | proteolysis involved in cellular protein catabolic process | -10.112687 |
| GO:0032260 | response to jasmonic acid stimulus involved in jasmonic acid and ethylene-dependent systemic resistance | -8.751969 |
| GO:0016081 | synaptic vesicle docking | -8.178899 |
| GO:0048462 | carpel formation | -6.173514 |
| GO:0006508 | proteolysis | -5.348966 |
| GO:0006885 | regulation of pH | -4.363572 |
| GO:0080156 | mitochondrial mRNA modification | -4.352576 |
| GO:0071602 | phytosphingosine biosynthetic process | -4.167583 |
| GO:0009694 | jasmonic acid metabolic process | -3.855562 |
| GO:0043086 | negative regulation of catalytic activity | -3.708144 |
| GO:0030244 | cellulose biosynthetic process | -3.449424 |
| GO:0019761 | glucosinolate biosynthetic process | -3.391467 |
| GO:0018008 | N-terminal peptidyl-glycine N-myristoylation | -3.253926 |
| GO:0010064 | embryonic shoot morphogenesis | -3.253926 |
| GO:0016131 | brassinosteroid metabolic process | -3.208332 |
| GO:1902184 | negative regulation of shoot apical meristem development | -3.165687 |
| GO:0006812 | cation transport | -3.078937 |
| GO:0042273 | ribosomal large subunit biogenesis | -2.363144 |
| GO:0010500 | transmitting tissue development | -2.323910 |
| GO:0050434 | positive regulation of viral transcription | -2.302352 |
| GO:0071289 | cellular response to nickel ion | -2.302352 |
| GO:0010208 | pollen wall assembly | -2.288990 |
| GO:0042773 | ATP synthesis coupled electron transport | -2.166858 |
| GO:0080143 | regulation of amino acid export | -2.163578 |
| GO:0043153 | entrainment of circadian clock by photoperiod | -2.163578 |
| GO:0015990 | electron transport coupled proton transport | -2.163578 |
| GO:0046785 | microtubule polymerization | -1.922603 |
| GO:0032461 | positive regulation of protein oligomerization | -1.861507 |
| GO:0048658 | anther wall tapetum development | -1.861507 |
| GO:0006446 | regulation of translational initiation | -1.783246 |
| GO:0097480 | establishment of synaptic vesicle localization | -1.778068 |
| GO:0019471 | 4-hydroxyproline metabolic process | -1.716219 |
| GO:0018401 | peptidyl-proline hydroxylation to 4-hydroxy-L-proline | -1.716219 |
| GO:0090284 | positive regulation of protein glycosylation in Golgi | -1.640876 |
| GO:0042407 | cristae formation | -1.635329 |
| GO:1900140 | regulation of seedling development | -1.374861 |
| GO:0052472 | modulation by host of symbiont transcription | -1.358014 |
| GO:0010374 | stomatal complex development | -1.351927 |
| TermID | Name | Value |
|---|---|---|
| GO:0009083 | branched-chain amino acid catabolic process | -12.099651 |
| GO:1902418 | (+)-abscisic acid D-glucopyranosyl ester transmembrane transport | -12.065236 |
| GO:0098660 | inorganic ion transmembrane transport | -9.090653 |
| GO:0015700 | arsenite transport | -8.216962 |
| GO:1901684 | arsenate ion transmembrane transport | -7.927843 |
| GO:0040007 | growth | -7.168854 |
| GO:0090284 | positive regulation of protein glycosylation in Golgi | -6.355361 |
| GO:0071669 | plant-type cell wall organization or biogenesis | -5.783306 |
| GO:0007059 | chromosome segregation | -5.267361 |
| GO:0043617 | cellular response to sucrose starvation | -4.682327 |
| GO:0007018 | microtubule-based movement | -4.630782 |
| GO:0009313 | oligosaccharide catabolic process | -4.522609 |
| GO:0090303 | positive regulation of wound healing | -4.515170 |
| GO:2000114 | regulation of establishment of cell polarity | -4.303925 |
| GO:1902198 | 3-methylbut-2-enoyl-CoA(4-) metabolic process | -3.727762 |
| GO:1904211 | membrane protein proteolysis involved in retrograde protein transport,ER to cytosol | -3.727762 |
| GO:0043007 | maintenance of rDNA | -3.677400 |
| GO:1900400 | regulation of iron ion import into cell by regulation of transcription from RNA polymerase II promoter | -3.277240 |
| GO:1901255 | nucleotide-excision repair involved in interstrand cross-link repair | -3.277240 |
| GO:0008347 | glial cell migration | -3.277240 |
| GO:0032508 | DNA duplex unwinding | -3.131414 |
| GO:0034260 | negative regulation of GTPase activity | -3.043832 |
| GO:0010104 | regulation of ethylene-activated signaling pathway | -2.878893 |
| GO:0030837 | negative regulation of actin filament polymerization | -2.774984 |
| GO:0097502 | mannosylation | -2.734209 |
| GO:1900153 | positive regulation of nuclear-transcribed mRNA catabolic process,deadenylation-dependent decay | -2.645697 |
| GO:1900049 | regulation of histone exchange | -2.607858 |
| GO:0097193 | intrinsic apoptotic signaling pathway | -2.601213 |
| GO:0000913 | preprophase band assembly | -2.495797 |
| GO:0016573 | histone acetylation | -2.305824 |
| GO:0009556 | microsporogenesis | -2.080502 |
| GO:0006075 | (1->3)-beta-D-glucan biosynthetic process | -1.868028 |
| GO:0071329 | cellular response to sucrose stimulus | -1.827140 |
| GO:0051289 | protein homotetramerization | -1.755497 |
| GO:0009624 | response to nematode | -1.749373 |
| GO:0106004 | tRNA (guanine-N7)-methylation | -1.563561 |
| GO:1900000 | regulation of anthocyanin catabolic process | -1.563561 |
| GO:0097242 | amyloid-beta clearance | -1.533347 |
| GO:0010992 | ubiquitin recycling | -1.533347 |
| GO:0008340 | determination of adult lifespan | -1.533347 |
| GO:0010815 | bradykinin catabolic process | -1.533347 |
| GO:0010208 | pollen wall assembly | -1.374147 |
| GO:0035194 | post-transcriptional gene silencing by RNA | -1.312663 |
| TermID | Name | Value |
|---|---|---|
| GO:0051603 | proteolysis involved in cellular protein catabolic process | -9.343439 |
| GO:0071482 | cellular response to light stimulus | -4.060248 |
| GO:0080156 | mitochondrial mRNA modification | -3.977341 |
| GO:0046785 | microtubule polymerization | -3.919147 |
| GO:0006624 | vacuolar protein processing | -3.194610 |
| GO:0006597 | spermine biosynthetic process | -3.169700 |
| GO:1990019 | protein storage vacuole organization | -2.561493 |
| GO:0030174 | regulation of DNA-dependent DNA replication initiation | -2.463341 |
| GO:0042372 | phylloquinone biosynthetic process | -2.463341 |
| GO:0046900 | tetrahydrofolylpolyglutamate metabolic process | -1.766281 |
| GO:0070914 | UV-damage excision repair | -1.765542 |
| GO:0071332 | cellular response to fructose stimulus | -1.444683 |
| GO:0010157 | response to chlorate | -1.444683 |
| TermID | Name | Value |
|---|---|---|
| GO:0005983 | starch catabolic process | -2.055820 |
| GO:0034721 | histone H3-K4 demethylation,trimethyl-H3-K4-specific | -1.884385 |
| GO:0046686 | response to cadmium ion | -1.754551 |
| GO:0071333 | cellular response to glucose stimulus | -1.582738 |
| GO:0030174 | regulation of DNA-dependent DNA replication initiation | -1.307768 |
| TermID | Name | Value |
|---|---|---|
| GO:0051603 | proteolysis involved in cellular protein catabolic process | -23.445501 |
| GO:0046785 | microtubule polymerization | -13.774183 |
| GO:0006624 | vacuolar protein processing | -9.895786 |
| GO:1990019 | protein storage vacuole organization | -8.591400 |
| GO:0080156 | mitochondrial mRNA modification | -7.414447 |
| GO:0010157 | response to chlorate | -5.513515 |
| GO:0048281 | inflorescence morphogenesis | -4.588824 |
| GO:0032989 | cellular component morphogenesis | -4.508650 |
| GO:0090156 | cellular sphingolipid homeostasis | -4.494330 |
| GO:0010090 | trichome morphogenesis | -4.097280 |
| GO:1901332 | negative regulation of lateral root development | -2.847257 |
| GO:0006278 | RNA-dependent DNA biosynthetic process | -2.761258 |
| GO:0032197 | transposition,RNA-mediated | -2.708915 |
| GO:0010286 | heat acclimation | -2.016484 |
| GO:0090709 | regulation of timing of plant organ formation | -1.857388 |
| GO:0006537 | glutamate biosynthetic process | -1.818101 |
| GO:0090305 | nucleic acid phosphodiester bond hydrolysis | -1.818070 |
| GO:0048194 | Golgi vesicle budding | -1.775108 |
| GO:0009408 | response to heat | -1.548177 |
| GO:0045332 | phospholipid translocation | -1.546385 |
| GO:0015770 | sucrose transport | -1.318982 |
| TermID | Name | Value |
|---|---|---|
| GO:0090284 | positive regulation of protein glycosylation in Golgi | -5.506616 |
| GO:0010222 | stem vascular tissue pattern formation | -5.047945 |
| GO:0008347 | glial cell migration | -4.650340 |
| GO:0090303 | positive regulation of wound healing | -4.387055 |
| GO:0040007 | growth | -4.373448 |
| GO:1900049 | regulation of histone exchange | -4.140205 |
| GO:2000114 | regulation of establishment of cell polarity | -3.856587 |
| GO:0043007 | maintenance of rDNA | -3.318770 |
| GO:2001240 | negative regulation of extrinsic apoptotic signaling pathway in absence of ligand | -2.928272 |
| GO:0046328 | regulation of JNK cascade | -2.672143 |
| GO:0080119 | ER body organization | -2.146026 |
| GO:0007030 | Golgi organization | -1.799156 |
| GO:0034260 | negative regulation of GTPase activity | -1.793183 |
| GO:0046459 | short-chain fatty acid metabolic process | -1.740640 |
| GO:0006336 | DNA replication-independent chromatin assembly | -1.395115 |
| TermID | Name | Value |
|---|---|---|
| GO:0071577 | zinc ion transmembrane transport | -6.945551 |
| GO:0000398 | mRNA splicing,via spliceosome | -6.679986 |
| GO:0010252 | auxin homeostasis | -4.110544 |
| GO:0006886 | intracellular protein transport | -4.096642 |
| GO:0006334 | nucleosome assembly | -3.942266 |
| GO:0006487 | protein N-linked glycosylation | -2.841110 |
| GO:0009637 | response to blue light | -2.750609 |
| GO:0034599 | cellular response to oxidative stress | -2.436697 |
| GO:0009658 | chloroplast organization | -2.279829 |
| GO:1903508 | positive regulation of nucleic acid-templated transcription | -2.028043 |
| GO:0006412 | translation | -1.833720 |
| GO:0045454 | cell redox homeostasis | -1.787827 |
| GO:0019915 | lipid storage | -1.718930 |
| GO:0015770 | sucrose transport | -1.566032 |
| GO:0000290 | deadenylation-dependent decapping of nuclear-transcribed mRNA | -1.465894 |
| GO:0008333 | endosome to lysosome transport | -1.454659 |
| GO:1902358 | sulfate transmembrane transport | -1.365088 |
| GO:0009853 | photorespiration | -1.311822 |
Let’s have a look at all of these plots. Manually zooming in leads to ggrepel reloading labels, so on the small scale a lot of these plots don’t have labels.
for(i in names(plot_list)) {
file_name = paste('output/', i, '.png', sep='')
cowplot::save_plot(file_name, plot_list[[i]], base_height=6)
}Let me also try and make some patchworks.
# For some reason with this plot the legends aren't correctly collected by patchwork,
# so I need to manually turn one off
patchy <- (plot_list[["GO_results_genes_in_Terrestrials_NOT_Aquatics_NOT_Seagrasses.csv"]] + theme(legend.position = "none")) /
plot_list[["GO_results_genes_union_Aquatics_and_Seagrasses_NOT_Terrestrials.csv"]] + plot_layout(guides = 'collect') + plot_annotation(tag_levels = 'A')
patchy
cowplot::save_plot('output/GO_results_terrestrials_vs_union_aquatics_seagrasses.png', patchy, base_height=7)OK I’ll better make this figure for the seagrasses alone, it’s quite messy this way.
Seagrass-specific loss
Let’s check which GO terms overlap between the 4 seagrasses!
How many shared lost GO-terms are there?
a <- list(`P. australis` = results_list$GO_results_genes_lost_P_australis_not_other_seagrasses.csv$Name,
`A. antarctica` = results_list$GO_results_genes_lost_A_antarctica_not_other_seagrasses.csv$Name,
`Z. marina` = results_list$GO_results_genes_lost_Z_marina_not_other_seagrasses.csv$Name,
`Z. muelleri` = results_list$GO_results_genes_lost_Z_muelleri_not_other_seagrasses.csv$Name)
a_go_ids <- list(`P. australis` = results_list$GO_results_genes_lost_P_australis_not_other_seagrasses.csv$TermID,
`A. antarctica` = results_list$GO_results_genes_lost_A_antarctica_not_other_seagrasses.csv$TermID,
`Z. marina` = results_list$GO_results_genes_lost_Z_marina_not_other_seagrasses.csv$TermID,
`Z. muelleri` = results_list$GO_results_genes_lost_Z_muelleri_not_other_seagrasses.csv$TermID)plot(venn(a),
quantities = TRUE,
fill = rev(wes_palette("Zissou1", 15, type = 'continuous')),
alpha = 0.5,
labels = list(font = 4))
upset(fromList(a), order.by='freq', )
a_no_ara <- list(`P. australis` = results_list$missing_posi_vs_all_GO.txt$Name,
`A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$Name,
`Z. marina` = results_list$missing_zmar_vs_all_GO.txt$Name,
`Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$Name)What are the shared GO-terms in seagrasses, WITHOUT the Ara loss??
Reduce(union, a) %>% enframe() %>% writexl::write_xlsx('./output/Seagrasses_shared_lost_genes.xlsx')What if we remove Posidonia?
b <- list(`A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$Name,
`Z. marina` = results_list$missing_zmar_vs_all_GO.txt$Name,
`Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$Name)
intersections <- Reduce(intersect, b)
intersections[grepl('ethylene', intersections)]NULLOK we need a big list of all GO-terms here - which GO-term is lost in which species. That will be a supplementary table.
all_species <- c("P. australis","A. antarctica","Z. marina","Z. muelleri", 'A. thaliana')
all_go_terms <- Reduce(union, a)
all_go_ids <- Reduce(union, a_go_ids)
results_d <- data.frame('GOID' = character(),
'GO' = character(),
'P. australis' = character(),
'A. antarctica' = character(),
'Z. marina' = character(),
'Z. muelleri' = character(),
'A. thaliana' = character())
for (index in seq_along(all_go_terms)){
go <- all_go_terms[index]
go_id <- all_go_ids[index]
specs <- c()
for (species in names(a)) {
if ( length(a[[species]][grep(paste('^', go, '$', sep=''), a[[species]])]) > 0 ) {
specs <- c(specs, species)
}
}
results_d[index,] <- c(go_id, go, gsub('FALSE', 'Present', gsub('TRUE', 'Lost', all_species %in% specs)))
}writexl::write_xlsx(results_d, 'output/Lost_GO_terms_in_five_species.xlsx')After filtering for plant-specific GO-terms
We will use the GO-terms that are plant-specific as identified by the GOMAP paper. See https://github.com/wkpalan/GOMAP-maize-analysis/blob/main/6.plantSpecific/1.getSppSpecific.R or https://plantmethods.biomedcentral.com/articles/10.1186/s13007-021-00754-1
go_plant <- read_tsv('https://raw.githubusercontent.com/wkpalan/GOMAP-maize-analysis/main/data/go/speciesSpecificGOTerms.txt')Rows: 45031 Columns: 5-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): GOterm
dbl (4): NCBITaxon:10090, NCBITaxon:33090, NCBITaxon:3702, NCBITaxon:40674
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.# taxon 33090 is Viridiplantae
plantSpecificGO <- go_plant %>% dplyr::filter(`NCBITaxon:33090`==1) %>% pull(GOterm)
plantSpecificGO <- c(plantSpecificGO,c("GO:0005575","GO:0008150","GO:0003674"))results_d %>% filter(GOID %in% plantSpecificGO) %>% writexl::write_xlsx('output/Lost_GO_terms_in_five_species.PlantSpecific.xlsx')Now let’s redo the Venn diagram with those filtered GO-terms
filters <- lapply(a_go_ids, function(ch) ch %in% plantSpecificGO)
newa <- list()
for (species in names(filters)) {
before <- a[[species]]
after <- before[filters[[species]]]
newa[[species]] <- after
}plot(venn(newa),
quantities = TRUE,
fill = rev(wes_palette("Zissou1", 15, type = 'continuous')),
alpha = 0.5,
labels = list(font = 4))
Not much difference?
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] patchwork_1.1.1 kableExtra_1.3.4 rrvgo_1.4.4
[4] UpSetR_1.4.0 eulerr_6.1.1 ggrepel_0.9.1
[7] stringi_1.7.5 httr_1.4.2 wesanderson_0.3.6
[10] rvest_1.0.2 forcats_0.5.1 stringr_1.4.0
[13] dplyr_1.0.7 purrr_0.3.4 readr_2.0.2
[16] tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5
[19] tidyverse_1.3.1 topGO_2.44.0 SparseM_1.81
[22] GO.db_3.13.0 AnnotationDbi_1.54.1 IRanges_2.26.0
[25] S4Vectors_0.30.2 Biobase_2.52.0 graph_1.70.0
[28] BiocGenerics_0.38.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] colorspace_2.0-2 ellipsis_0.3.2 rprojroot_2.0.2
[4] XVector_0.32.0 fs_1.5.0 rstudioapi_0.13
[7] farver_2.1.0 bit64_4.0.5 fansi_0.5.0
[10] lubridate_1.8.0 xml2_1.3.2 cachem_1.0.6
[13] GOSemSim_2.18.1 knitr_1.36 polyclip_1.10-0
[16] jsonlite_1.7.2 broom_0.7.9 gridBase_0.4-7
[19] dbplyr_2.1.1 png_0.1-7 pheatmap_1.0.12
[22] shiny_1.7.1 compiler_4.1.0 backports_1.2.1
[25] assertthat_0.2.1 fastmap_1.1.0 cli_3.0.1
[28] later_1.3.0 htmltools_0.5.2 tools_4.1.0
[31] igraph_1.2.7 NLP_0.2-1 gtable_0.3.0
[34] glue_1.4.2 GenomeInfoDbData_1.2.6 Rcpp_1.0.7
[37] slam_0.1-48 cellranger_1.1.0 jquerylib_0.1.4
[40] vctrs_0.3.8 Biostrings_2.60.2 writexl_1.4.0
[43] svglite_2.1.0 polylabelr_0.2.0 xfun_0.27
[46] mime_0.12 lifecycle_1.0.1 zlibbioc_1.38.0
[49] scales_1.1.1 treemap_2.4-3 vroom_1.5.5
[52] hms_1.1.1 promises_1.2.0.1 RColorBrewer_1.1-2
[55] curl_4.3.2 yaml_2.2.1 memoise_2.0.0
[58] gridExtra_2.3 sass_0.4.0 RSQLite_2.2.8
[61] highr_0.9 GenomeInfoDb_1.28.4 systemfonts_1.0.4
[64] rlang_0.4.12 pkgconfig_2.0.3 matrixStats_0.61.0
[67] bitops_1.0-7 evaluate_0.14 lattice_0.20-44
[70] labeling_0.4.2 cowplot_1.1.1 bit_4.0.4
[73] tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1
[76] R6_2.5.1 generics_0.1.1 DBI_1.1.1
[79] pillar_1.6.4 haven_2.4.3 whisker_0.4
[82] withr_2.4.2 KEGGREST_1.32.0 RCurl_1.98-1.5
[85] modelr_0.1.8 crayon_1.4.1 wordcloud_2.6
[88] utf8_1.2.2 tzdb_0.1.2 rmarkdown_2.11
[91] grid_4.1.0 readxl_1.3.1 data.table_1.14.2
[94] blob_1.2.2 git2r_0.28.0 webshot_0.5.2
[97] reprex_2.0.1 digest_0.6.28 xtable_1.8-4
[100] tm_0.7-8 httpuv_1.6.3 munsell_0.5.0
[103] viridisLite_0.4.0 bslib_0.3.1