R-gene count comparisons
Philipp Bayer
2020-09-18
Last updated: 2022-03-30
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Knit directory: R_gene_analysis/
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This is the same analysis as first-analysis, but with total numbers, not percentages genes lost
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
library(tidyverse)
library(patchwork)
library(ggsci)
library(dabestr)
library(dabestr)
library(cowplot)
library(ggsignif)
library(ggforce)
theme_set(theme_cowplot())Introduction
npg_col = pal_npg("nrc")(9)
col_list <- c(`Wild`=npg_col[8],
Landrace = npg_col[3],
`Old cultivar`=npg_col[2],
`Modern cultivar`=npg_col[4])
pav_table <- read_tsv('./data/soybean_pan_pav.matrix_gene.txt.gz')NBS part
Let’s pull the NBS genes from the table
nbs <- read_tsv('./data/Lee.NBS.candidates.lst', col_names = c('Name', 'Class'))
nbs# A tibble: 486 x 2
Name Class
<chr> <chr>
1 UWASoyPan00953.t1 CN
2 GlymaLee.13G222900.1.p CN
3 GlymaLee.18G227000.1.p CN
4 GlymaLee.18G080600.1.p CN
5 GlymaLee.20G036200.1.p CN
6 UWASoyPan01876.t1 CN
7 UWASoyPan04211.t1 CN
8 GlymaLee.19G105400.1.p CN
9 GlymaLee.18G085100.1.p CN
10 GlymaLee.11G142600.1.p CN
# ... with 476 more rows# have to remove the .t1s
nbs$Name <- gsub('.t1','', nbs$Name)nbs_pav_table <- pav_table %>% filter(Individual %in% nbs$Name)
write_delim(nbs_pav_table, 'data/NBS_PAV.txt.gz', delim='\t')Are NLR genes more likely to be lost?
not_nbs_pav_table <- pav_table %>% filter(! Individual %in% nbs$Name)not_nbs_pav_table# A tibble: 50,928 x 1,111
Individual `AB-01` `AB-02` `BR-01` `BR-02` `BR-03` `BR-04` `BR-05` `BR-06`
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 GlymaLee.01G~ 1 1 1 1 1 1 1 1
2 GlymaLee.01G~ 1 1 1 1 1 1 1 1
3 GlymaLee.01G~ 1 1 1 1 1 1 1 1
4 GlymaLee.01G~ 1 1 1 1 1 1 1 1
5 GlymaLee.01G~ 1 1 1 1 1 1 1 1
6 GlymaLee.01G~ 1 1 1 1 1 1 1 1
7 GlymaLee.01G~ 1 1 1 1 1 1 1 1
8 GlymaLee.01G~ 1 1 1 1 1 1 1 1
9 GlymaLee.01G~ 1 1 1 1 1 1 1 1
10 GlymaLee.01G~ 1 1 1 1 1 1 1 1
# ... with 50,918 more rows, and 1,102 more variables: BR-07 <dbl>,
# BR-08 <dbl>, BR-09 <dbl>, BR-10 <dbl>, BR-11 <dbl>, BR-12 <dbl>,
# BR-13 <dbl>, BR-14 <dbl>, BR-15 <dbl>, BR-16 <dbl>, BR-17 <dbl>,
# BR-18 <dbl>, BR-20 <dbl>, BR-23 <dbl>, BR-24 <dbl>, BR-29 <dbl>,
# BR-30 <dbl>, BR-32 <dbl>, DT2000 <dbl>, ESS <dbl>, For <dbl>, HN001 <dbl>,
# HN002 <dbl>, HN003 <dbl>, HN004 <dbl>, HN005 <dbl>, HN006 <dbl>,
# HN007 <dbl>, HN008 <dbl>, HN009 <dbl>, HN010 <dbl>, HN011 <dbl>, ...Chisquare test - I need the number of non-NBS genes core + variable, and the number of NBS genes core + variable
not_nbs_pav_table$Individual <- NULL
var <- 0
core <- 0
for (row in 1:nrow(not_nbs_pav_table)) {
if (0 %in% not_nbs_pav_table[row,]) {
var <- var + 1
} else {
core <- core + 1
}
}There are var variable genes in the non-NBS genes, and core core genes in the non-NBS genes.
backup <- nbs_pav_table
nbs_pav_table$Individual <- NULL
nbsvar <- 0
nbscore <- 0
for (row in 1:nrow(nbs_pav_table)) {
if (0 %in% nbs_pav_table[row,]) {
nbsvar <- nbsvar + 1
} else {
nbscore <- nbscore + 1
}
}
nbs_pav_table <- backupThere are 166 variable genes in the NBS genes, and 320 core genes in the NBS genes.
test_df <- data.frame(nonnbs=c(var, core), nbs=c(nbsvar, nbscore))
test_df nonnbs nbs
1 6594 166
2 44334 320chisq.test(test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: test_df
X-squared = 187.77, df = 1, p-value < 2.2e-16OK, so there’s a statistically significant association between variable genes and NBS genes.
test_df$nbs <- test_df$nbs/sum(test_df$nbs)
test_df$nonnbs <- test_df$nonnbs/sum(test_df$nonnbs)
test_df nonnbs nbs
1 0.1294769 0.3415638
2 0.8705231 0.6584362The same with RLPs
rlp <- read_tsv('./data/Lee.RLP.candidates.lst', col_names = c('Name', 'Class', 'Subtype'))
# have to remove the .t1s
rlp$Name <- gsub('.t1','', rlp$Name)rlp_pav_table <- pav_table %>% filter(Individual %in% rlp$Name)backup <- rlp_pav_table
rlp_pav_table$Individual <- NULL
rlpvar <- 0
rlpcore <- 0
for (row in 1:nrow(rlp_pav_table)) {
if (0 %in% rlp_pav_table[row,]) {
rlpvar <- rlpvar + 1
} else {
rlpcore <- rlpcore + 1
}
}
rlp_pav_table <- backupThere are 55 variable genes in the RLP genes, and 125 core genes in the RLP genes.
test_df <- data.frame(nonrlp=c(var, core), rlp=c(rlpvar, rlpcore))
test_df nonrlp rlp
1 6594 55
2 44334 125chisq.test(test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: test_df
X-squared = 47.594, df = 1, p-value = 5.242e-12test_df$rlp <- test_df$rlp/sum(test_df$rlp)
test_df$nonrlp <- test_df$nonrlp/sum(test_df$nonrlp)
test_df nonrlp rlp
1 0.1294769 0.3055556
2 0.8705231 0.6944444The same with RLKs
rlk <- read_tsv('./data/Lee.RLK.candidates.lst', col_names = c('Name', 'Class', 'Subtype'))
rlk# A tibble: 1,173 x 3
Name Class Subtype
<chr> <chr> <chr>
1 GlymaLee.01G001800.1.p RLK lrr
2 GlymaLee.01G004900.1.p RLK lrr
3 GlymaLee.01G007300.1.p RLK lrr
4 GlymaLee.01G007400.1.p RLK lrr
5 GlymaLee.01G012800.1.p RLK other_receptor
6 GlymaLee.01G018800.1.p RLK lrr
7 GlymaLee.01G021100.1.p RLK other_receptor
8 GlymaLee.01G025500.1.p RLK lysm
9 GlymaLee.01G026500.1.p RLK other_receptor
10 GlymaLee.01G027000.1.p RLK lrr
# ... with 1,163 more rows# have to remove the .t1s
rlk$Name <- gsub('.t1','', rlk$Name)rlk_pav_table <- pav_table %>% filter(Individual %in% rlk$Name)backup <- rlk_pav_table
rlk_pav_table$Individual <- NULL
rlkvar <- 0
rlkcore <- 0
for (row in 1:nrow(rlk_pav_table)) {
if (0 %in% rlk_pav_table[row,]) {
rlkvar <- rlkvar + 1
} else {
rlkcore <- rlkcore + 1
}
}
rlk_pav_table <- backupThere are 98 variable genes in the RLK genes, and 1075 core genes in the RLK genes.
test_df <- data.frame(nonrlk=c(var, core), rlk=c(rlkvar, rlkcore))chisq.test(test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: test_df
X-squared = 21.199, df = 1, p-value = 4.14e-06test_df$rlk <- test_df$rlk/sum(test_df$rlk)
test_df$nonrlk <- test_df$nonrlk/sum(test_df$nonrlk)
test_df nonrlk rlk
1 0.1294769 0.08354646
2 0.8705231 0.91645354The correct test - non-RGA vs NLR, RLP, RLK
The problem in the above calculations is that I still include the counts of NLR in the non-RPK genes, for example. Do the chisquare-tests come out differently if I remove the NLR/RLK/RLP counts from the non-RGA counts?
truecore <- core - (rlkcore + rlpcore + nbscore)
truevar <- var - (rlkvar + rlpvar + nbsvar)rlk_test_df <- data.frame(var = c(rlkvar, truevar), core = c(rlkcore, truecore))
chisq.test(rlk_test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: rlk_test_df
X-squared = 19.892, df = 1, p-value = 8.193e-06rlp_test_df <- data.frame(var = c(rlpvar, truevar), core = c(rlpcore, truecore))
chisq.test(rlp_test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: rlp_test_df
X-squared = 49.017, df = 1, p-value = 2.538e-12nlr_test_df <- data.frame(var = c(nbsvar, truevar), core = c(nbscore, truecore))
chisq.test(nlr_test_df)
Pearson's Chi-squared test with Yates' continuity correction
data: nlr_test_df
X-squared = 192.59, df = 1, p-value < 2.2e-16OK - they’re still p < 0.05
A quick check since we ran three tests:
p.adjust(c(8.193e-06, 2.538e-12, 2.2e-16), method = 'bonferroni')[1] 2.4579e-05 7.6140e-12 6.6000e-16Still p < 0.05 in all cases
Modern vs Old gene loss
groups <- read_csv('./data/Table_of_cultivar_groups.csv')
groups# A tibble: 1,069 x 3
`Data-storage-ID` `PI-ID` `Group in violin table`
<chr> <chr> <chr>
1 SRR1533284 PI416890 landrace
2 SRR1533282 PI323576 landrace
3 SRR1533292 PI157421 landrace
4 SRR1533216 PI594615 landrace
5 SRR1533239 PI603336 landrace
6 USB-108 PI165675 landrace
7 HNEX-13 PI253665D landrace
8 USB-382 PI603549 landrace
9 SRR1533236 PI587552 landrace
10 SRR1533332 PI567293 landrace
# ... with 1,059 more rowsWhich genes are present more or less in old / modern cultivars?
big_norm_count <- tibble(
name = character(),
landrace = numeric(),
Modern_cultivar = numeric(),
Old_cultivar = numeric(),
`Wild` = numeric()
)
groups_list <- split(groups$`Group in violin table`, groups$`Data-storage-ID`)
for( i in 1:nrow(nbs_pav_table) ) {
this_gene <- nbs_pav_table[i,]
groups_count <- list()
total_groups_count <- list()
for (x in seq_along(nbs_pav_table)){
if ( x == 1) next
thisind <- colnames(nbs_pav_table)[x]
thisind_group <- groups_list[[thisind]]
if( is.null(thisind_group) ) next # no group for this individual
pavs <- this_gene[[x]] # either 1 or 0
if ( thisind_group %in% names(groups_count)) {
# count the number of present genes
groups_count[[thisind_group]] <- groups_count[[thisind_group]] + pavs
# count the total number of individuals for this group
total_groups_count[[thisind_group]] <- total_groups_count[[thisind_group]] + 1
} else {
groups_count[[thisind_group]] <- pavs
total_groups_count[[thisind_group]] <- 1
}
}
norm_group_count <- list()
for (m in seq_along(groups_count)) {
thisname <- names(groups_count)[m]
norm_group_count[[thisname]] <- groups_count[[thisname]] / total_groups_count[[thisname]] * 100
}
norm_group_count$Individual <- this_gene$Individual
big_norm_count <- rbind(big_norm_count, as_tibble(norm_group_count))
}
# wow, I DO write R like PythonLet’s pull out the genes that are variable in any group
var_norm_count <- big_norm_count %>%
filter(landrace != 100 &
Modern_cultivar != 100 &
Old_cultivar != 100 &
`Wild-type` != 100)
var_norm_count <- left_join(var_norm_count, nbs, by=c('Individual'='Name'))
var_norm_count$Mod_minus_Old <- var_norm_count$Modern_cultivar - var_norm_count$Old_cultivarThe top 20 genes reduced the most in modern cultivars compared with old cultivars:
var_norm_count %>%
arrange(Mod_minus_Old) %>%
head(20) %>%
select(Individual, `Wild-type`, landrace, Old_cultivar, Modern_cultivar, Mod_minus_Old, Class) %>%
knitr::kable()| Individual | Wild-type | landrace | Old_cultivar | Modern_cultivar | Mod_minus_Old | Class |
|---|---|---|---|---|---|---|
| UWASoyPan03261 | 74.52229 | 62.102351 | 60.86957 | 26.573427 | -34.296139 | TX |
| UWASoyPan00953 | 83.43949 | 33.056708 | 43.47826 | 11.188811 | -32.289450 | CN |
| UWASoyPan00725 | 89.17197 | 92.392808 | 82.60870 | 51.748252 | -30.860444 | TX |
| UWASoyPan00316 | 91.08280 | 90.594744 | 80.43478 | 50.349650 | -30.085132 | NBS |
| UWASoyPan01530 | 80.89172 | 45.089903 | 47.82609 | 20.979021 | -26.847066 | NL |
| UWASoyPan00975 | 42.67516 | 19.778700 | 32.60870 | 7.692308 | -24.916388 | TX |
| UWASoyPan00155 | 85.35032 | 77.316736 | 63.04348 | 42.657343 | -20.386136 | NBS |
| UWASoyPan00772 | 54.77707 | 18.948824 | 30.43478 | 11.888112 | -18.546671 | NBS |
| UWASoyPan03402 | 62.42038 | 42.738589 | 36.95652 | 18.881119 | -18.075403 | NBS |
| UWASoyPan01320 | 45.85987 | 30.152144 | 23.91304 | 6.993007 | -16.920036 | NBS |
| UWASoyPan02799 | 65.60510 | 30.843707 | 19.56522 | 2.797203 | -16.768015 | NBS |
| GlymaLee.03G045500.1.p | 82.16561 | 58.921162 | 67.39130 | 51.748252 | -15.643053 | OTHER |
| UWASoyPan01253 | 73.24841 | 24.481328 | 17.39130 | 3.496504 | -13.894801 | NBS |
| UWASoyPan03340 | 18.47134 | 26.279391 | 19.56522 | 6.293706 | -13.271511 | TX |
| GlymaLee.06G230600.1.p | 78.34395 | 57.399723 | 56.52174 | 44.055944 | -12.465795 | TX |
| GlymaLee.06G228900.1.p | 96.17834 | 74.688797 | 91.30435 | 80.419580 | -10.884767 | TX |
| UWASoyPan00251 | 60.50955 | 20.470263 | 21.73913 | 11.188811 | -10.550319 | NL |
| GlymaLee.03G045700.1.p | 75.79618 | 67.496542 | 65.21739 | 55.244755 | -9.972636 | OTHER |
| GlymaLee.06G228600.1.p | 90.44586 | 79.391425 | 82.60870 | 72.727273 | -9.881423 | TX |
| UWASoyPan00670 | 30.57325 | 6.915629 | 10.86957 | 2.097902 | -8.771663 | TX |
So these are the NLR genes selected against during soybean breeding.
Let’s look at those without the TX ones:
var_norm_count %>%
arrange(Mod_minus_Old) %>%
select(Individual, `Wild-type`, landrace, Old_cultivar, Modern_cultivar, Mod_minus_Old, Class) %>%
filter(Class != 'TX') %>%
head(20) %>%
knitr::kable()| Individual | Wild-type | landrace | Old_cultivar | Modern_cultivar | Mod_minus_Old | Class |
|---|---|---|---|---|---|---|
| UWASoyPan00953 | 83.439490 | 33.0567082 | 43.478261 | 11.188811 | -32.289450 | CN |
| UWASoyPan00316 | 91.082802 | 90.5947441 | 80.434783 | 50.349650 | -30.085132 | NBS |
| UWASoyPan01530 | 80.891720 | 45.0899032 | 47.826087 | 20.979021 | -26.847066 | NL |
| UWASoyPan00155 | 85.350319 | 77.3167358 | 63.043478 | 42.657343 | -20.386136 | NBS |
| UWASoyPan00772 | 54.777070 | 18.9488243 | 30.434783 | 11.888112 | -18.546671 | NBS |
| UWASoyPan03402 | 62.420382 | 42.7385892 | 36.956522 | 18.881119 | -18.075403 | NBS |
| UWASoyPan01320 | 45.859873 | 30.1521438 | 23.913044 | 6.993007 | -16.920036 | NBS |
| UWASoyPan02799 | 65.605096 | 30.8437068 | 19.565217 | 2.797203 | -16.768015 | NBS |
| GlymaLee.03G045500.1.p | 82.165605 | 58.9211618 | 67.391304 | 51.748252 | -15.643053 | OTHER |
| UWASoyPan01253 | 73.248408 | 24.4813278 | 17.391304 | 3.496504 | -13.894801 | NBS |
| UWASoyPan00251 | 60.509554 | 20.4702628 | 21.739130 | 11.188811 | -10.550319 | NL |
| GlymaLee.03G045700.1.p | 75.796178 | 67.4965422 | 65.217391 | 55.244755 | -9.972636 | OTHER |
| UWASoyPan03194 | 45.222930 | 10.7883817 | 10.869565 | 2.097902 | -8.771663 | NBS |
| GlymaLee.03G045900.1.p | 74.522293 | 65.5601660 | 63.043478 | 54.545454 | -8.498024 | OTHER |
| UWASoyPan00326 | 40.764331 | 19.0871369 | 17.391304 | 9.790210 | -7.601095 | CN |
| UWASoyPan02496 | 26.114650 | 14.6611342 | 13.043478 | 6.993007 | -6.050471 | CN |
| UWASoyPan01217 | 57.961783 | 14.3845090 | 10.869565 | 5.594406 | -5.275160 | NBS |
| GlymaLee.06G229300.1.p | 86.624204 | 50.3457815 | 65.217391 | 60.839161 | -4.378230 | TN |
| UWASoyPan04757 | 6.369427 | 0.9681881 | 4.347826 | 0.000000 | -4.347826 | NBS |
| GlymaLee.03G042000.1.p | 99.363057 | 88.3817427 | 91.304348 | 88.111888 | -3.192460 | CNL |
Let’s plot:
var_norm_count %>%
arrange(Mod_minus_Old) %>%
head(20) %>%
select(Individual, `Wild-type`, landrace, Old_cultivar, Modern_cultivar, Class) %>%
pivot_longer(!c(Individual, Class)) %>%
mutate(name = str_replace_all(name, 'landrace', 'Landrace')) %>%
mutate(name = str_replace_all(name, 'Wild-type', 'Wild')) %>%
mutate(name = str_replace_all(name, 'Old_cultivar', 'Old cultivar')) %>%
mutate(name = str_replace_all(name, 'Modern_cultivar', 'Modern cultivar')) %>%
ggplot(aes(x=factor(name, levels=c('Wild', 'Landrace', 'Old cultivar', 'Modern cultivar')), y=value, group=Individual, color=Class)) +
geom_line(size=1.5) +
xlab('Group') +
ylab('Percentage presence of gene in group') +
scale_color_brewer(palette = 'Dark2')
The top 20 genes increased the most in modern cultivars:
var_norm_count %>%
arrange(desc(Mod_minus_Old)) %>%
head(20) %>%
select(Individual, `Wild-type`, landrace, Old_cultivar, Modern_cultivar, Mod_minus_Old, Class) %>%
knitr::kable()| Individual | Wild-type | landrace | Old_cultivar | Modern_cultivar | Mod_minus_Old | Class |
|---|---|---|---|---|---|---|
| GlymaLee.01G030900.1.p | 81.52866 | 50.345782 | 34.782609 | 71.328671 | 36.546063 | NL |
| GlymaLee.15G199500.1.p | 85.98726 | 73.582296 | 69.565217 | 86.713287 | 17.148069 | CN |
| GlymaLee.15G199200.1.p | 92.99363 | 74.827109 | 73.913044 | 90.909091 | 16.996047 | CNL |
| GlymaLee.06G232800.1.p | 40.12739 | 47.579530 | 56.521739 | 73.426573 | 16.904834 | NBS |
| GlymaLee.01G088400.1.p | 49.68153 | 89.488243 | 82.608696 | 97.202797 | 14.594102 | TNL |
| UWASoyPan05312 | 30.57325 | 8.575380 | 10.869565 | 23.776224 | 12.906659 | NBS |
| UWASoyPan00005 | 36.94268 | 13.831259 | 8.695652 | 20.279720 | 11.584068 | NBS |
| UWASoyPan01876 | 43.31210 | 15.629322 | 8.695652 | 20.279720 | 11.584068 | CN |
| GlymaLee.10G034600.1.p | 91.08280 | 91.839557 | 84.782609 | 95.104895 | 10.322286 | NL |
| UWASoyPan01330 | 29.29936 | 25.172891 | 15.217391 | 23.776224 | 8.558832 | NBS |
| UWASoyPan00202 | 50.31847 | 35.408022 | 26.086956 | 32.167832 | 6.080876 | NBS |
| UWASoyPan00427 | 97.45223 | 84.232365 | 73.913044 | 79.720280 | 5.807236 | NBS |
| GlymaLee.15G199300.1.p | 96.17834 | 88.243430 | 93.478261 | 98.601399 | 5.123138 | NL |
| GlymaLee.03G070700.1.p | 65.60510 | 89.903181 | 89.130435 | 93.706294 | 4.575859 | TNL |
| GlymaLee.06G229100.1.p | 85.98726 | 38.174274 | 50.000000 | 53.146853 | 3.146853 | TX |
| GlymaLee.07G070200.1.p | 78.98089 | 91.286307 | 91.304348 | 94.405594 | 3.101247 | NBS |
| UWASoyPan01418 | 68.78981 | 66.251729 | 71.739130 | 74.825175 | 3.086044 | TX |
| GlymaLee.03G070600.1.p | 66.87898 | 90.179806 | 91.304348 | 93.706294 | 2.401946 | TNL |
| GlymaLee.16G175200.1.p | 95.54140 | 96.127248 | 95.652174 | 97.902098 | 2.249924 | TNL |
| UWASoyPan04967 | 35.03185 | 6.224066 | 2.173913 | 4.195804 | 2.021891 | TX |
As these genes have relatively high percentages in WT they must have been re-introduced by using WT in the breeding process.
Let’s plot those too:
var_norm_count %>%
arrange(desc(Mod_minus_Old)) %>%
head(20) %>%
select(Individual, `Wild-type`, landrace, Old_cultivar, Modern_cultivar, Class) %>%
pivot_longer(!c(Individual, Class)) %>%
mutate(name = str_replace_all(name, 'landrace', 'Landrace')) %>%
mutate(name = str_replace_all(name, 'Old_cultivar', 'Old cultivar')) %>%
mutate(name = str_replace_all(name, 'Modern_cultivar', 'Modern cultivar')) %>%
mutate(name = str_replace_all(name, 'Wild-type', 'Wild')) %>%
ggplot(aes(x=factor(name, levels=c('Wild', 'Landrace', 'Old cultivar', 'Modern cultivar')), y=value, group=Individual, color=Class)) +
geom_line(size=1.5) +
xlab('Group') +
ylab('Percentage presence of gene in group') +
scale_color_brewer(palette = 'Dark2')
Presence plotting per individual
names <- c()
presences <- c()
for (i in seq_along(nbs_pav_table)){
if ( i == 1) next
thisind <- colnames(nbs_pav_table)[i]
pavs <- nbs_pav_table[[i]]
presents <- sum(pavs)
names <- c(names, thisind)
presences <- c(presences, presents)
}
nbs_res_tibb <- new_tibble(list(names = names, presences = presences))OK what do these presence percentages look like?
ggplot(data=nbs_res_tibb, aes(x=presences)) + geom_histogram(bins=25) 
On average, 446.0027027 of NBS genes are present in each individual.
Now let’s join the table of presences to the four different types so we can group these numbers.
nbs_joined_groups <- left_join(nbs_res_tibb, groups, by = c('names'='Data-storage-ID'))nbs_joined_groups$`Group in violin table` <- gsub('landrace', 'Landrace', nbs_joined_groups$`Group in violin table`)
nbs_joined_groups$`Group in violin table` <- gsub('Modern_cultivar', 'Modern cultivar', nbs_joined_groups$`Group in violin table`)
nbs_joined_groups$`Group in violin table` <- gsub('Old_cultivar', 'Old cultivar', nbs_joined_groups$`Group in violin table`)
nbs_joined_groups$`Group in violin table` <- gsub('Wild-type', 'Wild', nbs_joined_groups$`Group in violin table`)
nbs_joined_groups$`Group in violin table` <- factor(nbs_joined_groups$`Group in violin table`, levels=c(NA, 'Wild', 'Landrace', 'Old cultivar', 'Modern cultivar'))nbs_vio <- nbs_joined_groups %>% filter(!is.na(`Group in violin table`)) %>%
ggplot(aes(y=presences, x=`Group in violin table`, fill=`Group in violin table`)) +
geom_violin(draw_quantiles = c(0.5)) +
geom_sina(alpha=0.5) +
geom_smooth(aes(group=1), method='glm') +
scale_fill_manual(values=col_list) +
guides(fill = FALSE)
nbs_vio
nbs_joined_groups %>% filter(`Group in violin table` != 'NA') %>%
ggplot(aes(y=presences, x=`Group in violin table`, fill=`Group in violin table`)) +
geom_smooth(aes(group=1), method='lm', se = FALSE) +
geom_jitter() +
scale_fill_manual(values=col_list)+
guides(fill = FALSE)
nbs_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
group_by(`Group in violin table`) %>%
summarise(min_present = min(presences),
max_present = max(presences),
mean_present = mean(presences),
median_present = median(presences),
std_present = sd(presences)) %>%
knitr::kable()| Group in violin table | min_present | max_present | mean_present | median_present | std_present |
|---|---|---|---|---|---|
| Wild | 435 | 473 | 452.9490 | 453 | 7.170806 |
| Landrace | 429 | 465 | 444.8907 | 445 | 5.011672 |
| Old cultivar | 433 | 456 | 444.8696 | 445 | 5.200892 |
| Modern cultivar | 431 | 455 | 442.3147 | 442 | 4.047986 |
RLK part
Let’s do the same plot with RLKs
names <- c()
presences <- c()
for (i in seq_along(rlk_pav_table)){
if ( i == 1) next
thisind <- colnames(rlk_pav_table)[i]
pavs <- rlk_pav_table[[i]]
presents <- sum(pavs)
names <- c(names, thisind)
presences <- c(presences, presents)
}
rlk_res_tibb <- new_tibble(list(names = names, presences = presences))
rlk_res_tibb# A tibble: 1,110 x 2
names presences
<chr> <dbl>
1 AB-01 1167
2 AB-02 1162
3 BR-01 1166
4 BR-02 1165
5 BR-03 1166
6 BR-04 1167
7 BR-05 1164
8 BR-06 1167
9 BR-07 1165
10 BR-08 1167
# ... with 1,100 more rowsOK what do these presence percentages look like?
ggplot(data=rlk_res_tibb, aes(x=presences)) + geom_histogram(bins=25) 
On average, 1163.5036036% of NBS genes are present in each individual.
Now let’s join the table of presences to the four different types so we can group these numbers.
rlk_joined_groups <- left_join(rlk_res_tibb, groups, by = c('names'='Data-storage-ID'))rlk_joined_groups$`Group in violin table` <- gsub('landrace', 'Landrace', rlk_joined_groups$`Group in violin table`)
rlk_joined_groups$`Group in violin table` <- gsub('Modern_cultivar', 'Modern cultivar', rlk_joined_groups$`Group in violin table`)
rlk_joined_groups$`Group in violin table` <- gsub('Old_cultivar', 'Old cultivar', rlk_joined_groups$`Group in violin table`)
rlk_joined_groups$`Group in violin table` <- gsub('Wild-type', 'Wild', rlk_joined_groups$`Group in violin table`)
rlk_joined_groups$`Group in violin table` <- factor(rlk_joined_groups$`Group in violin table`, levels=c(NA, 'Wild', 'Landrace', 'Old cultivar', 'Modern cultivar'))rlk_vio <- rlk_joined_groups %>% filter(`Group in violin table` != 'NA') %>%
ggplot(aes(y=presences, x=`Group in violin table`, fill=`Group in violin table`)) +
geom_violin(draw_quantiles = c(0.5)) +
geom_sina(alpha=0.5) +
geom_smooth(aes(group=1), method='lm', se = FALSE) +
scale_fill_manual(values=col_list)+
guides(fill = FALSE)
rlk_vio
rlk_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
group_by(`Group in violin table`) %>%
summarise(min_present = min(presences),
max_present = max(presences),
mean_present = mean(presences),
median_present = median(presences),
std_present = sd(presences)) %>%
knitr::kable()| Group in violin table | min_present | max_present | mean_present | median_present | std_present |
|---|---|---|---|---|---|
| Wild | 1154 | 1170 | 1164.357 | 1165 | 2.554565 |
| Landrace | 1157 | 1168 | 1163.217 | 1163 | 1.499264 |
| Old cultivar | 1161 | 1166 | 1163.587 | 1164 | 1.407537 |
| Modern cultivar | 1159 | 1168 | 1163.490 | 1163 | 1.472122 |
RLP part
And now with RLPs
names <- c()
presences <- c()
for (i in seq_along(rlp_pav_table)){
if ( i == 1) next
thisind <- colnames(rlp_pav_table)[i]
pavs <- rlp_pav_table[[i]]
presents <- sum(pavs)
names <- c(names, thisind)
presences <- c(presences, presents)
}
rlp_res_tibb <- new_tibble(list(names = names, presences = presences))OK what do these presence percentages look like?
ggplot(data=rlp_res_tibb, aes(x=presences)) + geom_histogram(bins=25) 
On average, 172.1693694% of NBS genes are present in each individual.
Now let’s join the table of presences to the four different types so we can group these numbers.
rlp_joined_groups <- left_join(rlp_res_tibb, groups, by = c('names'='Data-storage-ID'))rlp_joined_groups$`Group in violin table` <- gsub('landrace', 'Landrace', rlp_joined_groups$`Group in violin table`)
rlp_joined_groups$`Group in violin table` <- gsub('Modern_cultivar', 'Modern cultivar', rlp_joined_groups$`Group in violin table`)
rlp_joined_groups$`Group in violin table` <- gsub('Old_cultivar', 'Old cultivar', rlp_joined_groups$`Group in violin table`)
rlp_joined_groups$`Group in violin table` <- gsub('Wild-type', 'Wild', rlp_joined_groups$`Group in violin table`)
rlp_joined_groups$`Group in violin table` <- factor(rlp_joined_groups$`Group in violin table`, levels=c(NA, 'Wild', 'Landrace', 'Old cultivar', 'Modern cultivar'))rlp_vio <- rlp_joined_groups %>% filter(`Group in violin table` != 'NA') %>%
ggplot(aes(y=presences, x=`Group in violin table`, fill=`Group in violin table`)) +
geom_violin(draw_quantiles = c(0.5)) +
geom_sina(alpha=0.5) +
geom_smooth(aes(group=1), method='lm', se = FALSE) +
scale_fill_manual(values=col_list)+
guides(fill = FALSE)
rlp_vio
rlp_joined_groups %>% filter(`Group in violin table` != 'NA') %>%
ggplot(aes(y=presences, x=`Group in violin table`, fill=`Group in violin table`)) +
geom_jitter() +
#geom_sina(alpha=0.5) +
scale_fill_manual(values=col_list)+
guides(fill = FALSE) +
ylim(c(87, 100))
rlp_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
group_by(`Group in violin table`) %>%
summarise(min_present = min(presences),
max_present = max(presences),
mean_present = mean(presences),
median_present = median(presences),
std_present = sd(presences)) %>%
knitr::kable()| Group in violin table | min_present | max_present | mean_present | median_present | std_present |
|---|---|---|---|---|---|
| Wild | 168 | 177 | 173.4140 | 173 | 1.617392 |
| Landrace | 162 | 177 | 171.9668 | 172 | 1.661526 |
| Old cultivar | 169 | 176 | 171.8261 | 172 | 1.623499 |
| Modern cultivar | 169 | 175 | 171.8042 | 172 | 1.290587 |
Plotting together
nbs_vio + rlk_vio + rlp_vio
Stats - Dabayes
I want to know whether the groups are statistically significantly different. First let’s use dabestr
NBS
Let’s run dabestr first:
nbs_multi.two.group.unpaired <-
nbs_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
dabest(`Group in violin table`, presences,
idx = list(c("Wild", "Landrace"),
c('Old cultivar', 'Modern cultivar')),
paired = FALSE)
nbs_multi.two.group.unpaireddabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
The first five rows are:
# A tibble: 5 x 4
names presences `PI-ID` `Group in violin table`
<chr> <dbl> <chr> <fct>
1 AB-01 445 PI458020 Landrace
2 AB-02 454 PI603713 Landrace
3 DT2000 447 PI635999 Modern cultivar
4 For 448 PI548645 Modern cultivar
5 HN001 448 PI518664 Modern cultivar
X Variable : Group in violin table
Y Variable : presences
Effect sizes(s) will be computed for:
1. Landrace minus Wild
2. Modern cultivar minus Old cultivarnbs_multi.two.group.unpaired.meandiff <- mean_diff(nbs_multi.two.group.unpaired)
nbs_multi.two.group.unpaired.meandiffdabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
X Variable : Group in violin table
Y Variable : presences
Unpaired mean difference of Landrace (n = 723) minus Wild (n = 157)
-8.06 [95CI -9.24; -6.86]
Unpaired mean difference of Modern cultivar (n = 143) minus Old cultivar (n = 46)
-2.55 [95CI -4.25; -0.97]
5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.plot(nbs_multi.two.group.unpaired.meandiff, color.column=`Group in violin table`,
rawplot.ylabel = 'Presence (%)', show.legend=FALSE)
RLK
rlk_multi.two.group.unpaired <-
rlk_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
dabest(`Group in violin table`, presences,
idx = list(c("Wild", "Landrace"),
c('Old cultivar', 'Modern cultivar')),
paired = FALSE)
rlk_multi.two.group.unpaireddabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
The first five rows are:
# A tibble: 5 x 4
names presences `PI-ID` `Group in violin table`
<chr> <dbl> <chr> <fct>
1 AB-01 1167 PI458020 Landrace
2 AB-02 1162 PI603713 Landrace
3 DT2000 1165 PI635999 Modern cultivar
4 For 1163 PI548645 Modern cultivar
5 HN001 1163 PI518664 Modern cultivar
X Variable : Group in violin table
Y Variable : presences
Effect sizes(s) will be computed for:
1. Landrace minus Wild
2. Modern cultivar minus Old cultivarrlk_multi.two.group.unpaired.meandiff <- mean_diff(rlk_multi.two.group.unpaired)
rlk_multi.two.group.unpaired.meandiffdabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
X Variable : Group in violin table
Y Variable : presences
Unpaired mean difference of Landrace (n = 723) minus Wild (n = 157)
-1.14 [95CI -1.55; -0.717]
Unpaired mean difference of Modern cultivar (n = 143) minus Old cultivar (n = 46)
-0.0974 [95CI -0.562; 0.362]
5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.plot(rlk_multi.two.group.unpaired.meandiff, color.column=`Group in violin table`,
rawplot.ylabel = 'Presence (%)', show.legend=FALSE)
No difference between old and modern cultivars!
RLP
rlp_multi.two.group.unpaired <-
rlp_joined_groups %>% filter(!is.na(`PI-ID`)) %>%
dabest(`Group in violin table`, presences,
idx = list(c("Wild", "Landrace"),
c('Old cultivar', 'Modern cultivar')),
paired = FALSE)
rlp_multi.two.group.unpaireddabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
The first five rows are:
# A tibble: 5 x 4
names presences `PI-ID` `Group in violin table`
<chr> <dbl> <chr> <fct>
1 AB-01 171 PI458020 Landrace
2 AB-02 172 PI603713 Landrace
3 DT2000 171 PI635999 Modern cultivar
4 For 171 PI548645 Modern cultivar
5 HN001 172 PI518664 Modern cultivar
X Variable : Group in violin table
Y Variable : presences
Effect sizes(s) will be computed for:
1. Landrace minus Wild
2. Modern cultivar minus Old cultivarrlp_multi.two.group.unpaired.meandiff <- mean_diff(rlp_multi.two.group.unpaired)
rlp_multi.two.group.unpaired.meandiffdabestr (Data Analysis with Bootstrap Estimation in R) v0.3.0
=============================================================
Good evening!
The current time is 18:10 PM on Wednesday March 30, 2022.
Dataset : .
X Variable : Group in violin table
Y Variable : presences
Unpaired mean difference of Landrace (n = 723) minus Wild (n = 157)
-1.45 [95CI -1.74; -1.17]
Unpaired mean difference of Modern cultivar (n = 143) minus Old cultivar (n = 46)
-0.0219 [95CI -0.53; 0.477]
5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.plot(rlp_multi.two.group.unpaired.meandiff, color.column=`Group in violin table`,
rawplot.ylabel = 'Presence (%)', show.legend=FALSE)
Again, no difference between old and modern cultivars!
Stats - classic t-test
NBS
nlr_plot <- nbs_joined_groups %>%
filter( !is.na(`PI-ID`) ) %>%
ggplot(aes(x=`Group in violin table`, y = presences,
fill = `Group in violin table`)) +
geom_boxplot() +
scale_fill_manual(values = col_list) +
theme_minimal_hgrid() +
theme(axis.text.x = element_text(size=12),
axis.text.y = element_text(size=12)) +
geom_signif(comparisons = list(c('Wild', 'Landrace'),
c('Old cultivar', 'Modern cultivar')),
map_signif_level = T) +
guides(fill=FALSE) +
ylab('Number of NLR genes') +
xlab('Accession group')
nlr_plot
save(nlr_plot, file = 'output/NLR_boxplot_saved.Rds')RLP
rlp_joined_groups %>%
filter( !is.na(`PI-ID`) ) %>%
ggplot(aes(x=`Group in violin table`, y = presences,
fill = `Group in violin table`)) +
geom_boxplot() +
scale_fill_manual(values = col_list) +
theme_minimal_hgrid() +
theme(axis.text.x = element_text(size=12),
axis.text.y = element_text(size=12)) +
geom_signif(comparisons = list(c('Wild', 'Landrace'),
c('Old cultivar', 'Modern cultivar')),
map_signif_level = T) +
guides(fill=FALSE) +
ylab('Number of RLP genes') +
xlab('Accession group')
RLK
rlk_joined_groups %>%
filter( !is.na(`PI-ID`) ) %>%
ggplot(aes(x=`Group in violin table`, y = presences,
fill = `Group in violin table`)) +
geom_boxplot() +
scale_fill_manual(values = col_list) +
theme_minimal_hgrid() +
theme(axis.text.x = element_text(size=12),
axis.text.y = element_text(size=12)) +
geom_signif(comparisons = list(c('Wild', 'Landrace'),
c('Old cultivar', 'Modern cultivar')),
map_signif_level = T) +
guides(fill=FALSE) +
ylab('Number of RLK genes') +
xlab('Accession group')
Ratio of NLR/RLK plot
rlk_nbs_joined_groups <- rlk_joined_groups %>% inner_join(nbs_joined_groups, by=c('names'))
rlk_nbs_joined_groups$ratio <- rlk_nbs_joined_groups$presences.x / rlk_nbs_joined_groups$presences.y # RLK/NLR
rlk_nbs_joined_groups %>%
filter( !is.na(`PI-ID.x`) ) %>%
ggplot(aes(x=`Group in violin table.x`, y = ratio,
fill = `Group in violin table.x`)) +
geom_boxplot() +
scale_fill_manual(values = col_list) +
theme_minimal_hgrid() +
theme(axis.text.x = element_text(size=12),
axis.text.y = element_text(size=12)) +
geom_signif(comparisons = list(c('Wild', 'Landrace'),
c('Old cultivar', 'Modern cultivar')),
map_signif_level = T) +
guides(fill=FALSE) +
ylab('Number of RLK divided by NLR') +
xlab('Accession group')
Ratio of NLR/RLP plot
rlp_nbs_joined_groups <- rlp_joined_groups %>% inner_join(nbs_joined_groups, by=c('names'))
rlp_nbs_joined_groups$ratio <- rlp_nbs_joined_groups$presences.x / rlp_nbs_joined_groups$presences.y # RLP/NLR
rlp_nbs_joined_groups %>%
filter( !is.na(`PI-ID.x`) ) %>%
ggplot(aes(x=`Group in violin table.x`, y = ratio,
fill = `Group in violin table.x`)) +
geom_boxplot() +
scale_fill_manual(values = col_list) +
theme_minimal_hgrid() +
theme(axis.text.x = element_text(size=12),
axis.text.y = element_text(size=12)) +
geom_signif(comparisons = list(c('Wild', 'Landrace'),
c('Old cultivar', 'Modern cultivar')),
map_signif_level = T) +
guides(fill=FALSE) +
ylab('Number of RLP divided by NLR') +
xlab('Accession group')
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggforce_0.3.3 ggsignif_0.6.3 cowplot_1.1.1 dabestr_0.3.0
[5] magrittr_2.0.1 ggsci_2.9 patchwork_1.1.1 forcats_0.5.1
[9] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.2
[13] tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1
[17] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] nlme_3.1-152 fs_1.5.0 lubridate_1.8.0 bit64_4.0.5
[5] RColorBrewer_1.1-2 httr_1.4.2 rprojroot_2.0.2 tools_4.1.0
[9] backports_1.2.1 bslib_0.3.1 utf8_1.2.2 R6_2.5.1
[13] vipor_0.4.5 mgcv_1.8-35 DBI_1.1.1 colorspace_2.0-2
[17] withr_2.5.0 tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0
[21] git2r_0.28.0 cli_3.2.0 rvest_1.0.2 xml2_1.3.2
[25] labeling_0.4.2 sass_0.4.0 scales_1.1.1 digest_0.6.28
[29] rmarkdown_2.11 pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1
[33] fastmap_1.1.0 highr_0.9 rlang_0.4.12 readxl_1.3.1
[37] rstudioapi_0.13 jquerylib_0.1.4 farver_2.1.0 generics_0.1.1
[41] jsonlite_1.7.2 vroom_1.5.7 Matrix_1.3-3 ggbeeswarm_0.6.0
[45] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.1
[49] stringi_1.7.5 whisker_0.4 yaml_2.2.1 MASS_7.3-54
[53] plyr_1.8.6 grid_4.1.0 parallel_4.1.0 promises_1.2.0.1
[57] crayon_1.4.1 lattice_0.20-44 splines_4.1.0 haven_2.4.3
[61] hms_1.1.1 knitr_1.36 pillar_1.6.4 boot_1.3-28
[65] reprex_2.0.1 glue_1.6.2 evaluate_0.14 modelr_0.1.8
[69] vctrs_0.3.8 tzdb_0.1.2 tweenr_1.0.2 httpuv_1.6.3
[73] cellranger_1.1.0 gtable_0.3.0 polyclip_1.10-0 assertthat_0.2.1
[77] xfun_0.27 broom_0.7.9 later_1.3.0 beeswarm_0.4.0
[81] ellipsis_0.3.2