R: Updating Hover Text - r

I am using the R programming language. I made the following interactive graph using the plotly library:
library(dplyr)
library(ggplot2)
library(shiny)
library(plotly)
library(htmltools)
library(dplyr)
#generate data
set.seed(123)
######
var = rnorm(731, 85,25)
date= seq(as.Date("2014/1/1"), as.Date("2016/1/1"),by="day")
data = data.frame(var,date)
vals <- 90:100
combine <- vector('list', length(vals))
count <- 0
for (i in vals) {
data$var_i = i
data$new_var_i = ifelse(data$var >i,1,0)
#percent of observations greater than i (each month)
aggregate_i = data %>%
mutate(date = as.Date(date)) %>%
group_by(month = format(date, "%Y-%m")) %>%
summarise( mean = mean(new_var_i))
#combine files together
aggregate_i$var = i
aggregate_i$var = as.factor(aggregate_i$var)
count <- count + 1
combine[[count]] <- aggregate_i
}
result_2 <- bind_rows(combine)
result_2$group = "group_b"
result_2$group = as.factor(result_2$group)
graph <-ggplot(result_2, aes(frame = var, color = group)) + geom_line(aes(x=month, y=mean, group=1))+ theme(axis.text.x = element_text(angle=90)) + ggtitle("title") + facet_wrap(. ~ group)
graph = ggplotly(graph)
When the user moves the mouse over any point on the graph, the following information is displayed (hover text):
I am trying to add more information to the hover text. For example:
result_2$tot = mean(result_2$mean)
> head(result_2)
# A tibble: 6 x 5
month mean var group tot
<chr> <dbl> <fct> <fct> <dbl>
1 2014-01 0.387 90 group_b 0.364
2 2014-02 0.429 90 group_b 0.364
3 2014-03 0.452 90 group_b 0.364
4 2014-04 0.367 90 group_b 0.364
5 2014-05 0.355 90 group_b 0.364
6 2014-06 0.433 90 group_b 0.364
Yet, when I make a new graph using this result_2 file, the new information does not appear in the hover text:
graph <-ggplot(result_2, aes(frame = var, color = group)) + geom_line(aes(x=month, y=mean, group=1))+ theme(axis.text.x = element_text(angle=90)) + ggtitle("title") + facet_wrap(. ~ group)
graph = ggplotly(graph)
#view graph
graph
Can someone please shoe me how to fix this problem?
Thanks

If you want full control of your hoverinfo its actually best to create a plotly chart rather than a ggplot and then use ggplotly(). If you have only one group in result_2 as in your example above you can use
result_2 %>%
plot_ly(x=~month, y=~mean, color=~group) %>%
group_by(group) %>%
add_lines(frame=~var,hoverinfo = "text",
text = ~ paste0("Month: ",month, "<br>",
"Mean: ", mean, "<br>",
"Total: ", mean(mean))) %>%
layout(title = list(text = "title"),
xaxis = list(tickangle = -90, tickformat = "%m-%Y"))
or if you have > 1 group in result_2 and you want to facet by group as indicated in your ggplot you can do:
result_2 %>%
group_by(group) %>%
do(
plot = plot_ly(data =., x=~month, y=~mean, color=~group) %>%
add_lines(frame=~var,hoverinfo = "text",
text = ~ paste0("Month: ",month, "<br>",
"Mean: ", mean, "<br>",
"Total: ", mean(mean))) %>%
layout(title = list(text = "title"),
xaxis = list(tickangle = -90, tickformat = "%m-%Y"))
) %>%
subplot(shareX = TRUE, shareY = FALSE, nrows = 2)
But this won't work if you have only one group hence the two options provided.
You can create any function and write anything you want in the text = ~paste0() part and it will show up in your hoverinfo.

Related

gganimate does not stop at the defined value

Update: Sorry I forgot to add the vector:
time=1:100
value = 1:67
fill = rep(max(value), 100-max(value))
I want to make an animated stacked bar, Here is my example:
library(tidyverse)
library(gganimate)
#example data frame
df <- tibble(time = time,
value = c(value, fill),
x = "A") %>%
mutate(fill_color = "gold") %>%
mutate(gold_nr = value) %>%
mutate(blue_nr = rev(gold_nr)) %>%
pivot_longer(c(gold_nr, blue_nr),
names_to = "color_group",
values_to = "value_group")
# the code:
p <- df %>%
ggplot(aes("", value_group, fill=color_group)) +
geom_col(width = 0.3, position = position_fill())+
scale_fill_manual(values = c("gold", "steelblue"))+
theme_minimal()+
# theme(legend.position="none")+
transition_manual(value)+
coord_flip()
animate(p, fps=24, renderer = gifski_renderer(loop = FALSE))
My question is: Why does the bar not stop at 67 and jumps over 75?
I think I have to organize the data in a other way?
You should use time column to group the frames.
tail(df, 4)
# time fill_color color_group value_group
# 197 99 gold gold_nr 67
# 198 99 gold blue_nr 2
# 199 100 gold gold_nr 67
# 200 100 gold blue_nr 1
The plot now shows correctly the proportions in the last time frame.
proportions(df[df$time == 100, ]$value_group)
# [1] 0.98529412 0.01470588
library('magrittr')
p <- df %>%
ggplot2::ggplot(ggplot2::aes("", value_group, fill=color_group)) +
ggplot2::geom_col(width=0.3, position=position_fill()) +
ggplot2::scale_fill_manual(values=c("steelblue", "gold")) +
ggplot2::theme_minimal() +
ggplot2::coord_flip() +
gganimate::transition_manual(time)
a <- gganimate::animate(p, fps=24, renderer=gifski_renderer(loop=TRUE))
gganimate::anim_save('a.gif', a)
Note, that your colors were flipped.

How to visualize multiple bar plots in one (or splitted) pdf

I'm using the tidyverse-ggplot2 combination to plot multiple bar plots. In one of my comparisons i would like to have even up to 300 single plots. I was wondering if there is a possibility to make sure that the plots will be visible in the pdf file and not look like the attached example
If possible I would prefer to have all the plots in one single pdf file, but if not, also multiple pages will be ok.
The command to plot the bar charts is
common %>%
as_tibble(rownames="gene") %>%
left_join(x= ., y = up[,1:2], by = c("gene" = "ensembl_gene_id") ) %>%
pivot_longer(starts_with("S"), names_to="sample", values_to="counts") %>%
left_join(groups, by="sample") %>%
group_by(mgi_symbol, group, cond, time) %>%
summarize(mean_count=mean(counts)) %>%
ggplot( aes(x = time, y = mean_count, fill=cond)) +
geom_bar(stat = "identity", position = position_dodge(width=0.9) ) +
scale_fill_manual(values=c("darkblue", "lightblue", "black")) +
facet_wrap(~mgi_symbol, scales = "free", ncol = 5) +
theme_bw()
I forgot to add the group table
groups <- tibble(
sample= colnames(normCounts),
group = rep(seq(1, ncol(normCounts)/3), each=3),
cond = rep(c("WT", "GCN2-KO", "GCN1-KO"), each = 12),
time = rep(rep(c("0h", "1h", "4h", "8h"), each=3), times = 3 )
)
thanks
Adding the command with the group_map was as such
common %>%
as_tibble(rownames="gene") %>%
left_join(x= ., y = up[,1:2], by = c("gene" = "ensembl_gene_id") ) %>%
pivot_longer(starts_with("S"), names_to="sample", values_to="counts") %>%
left_join(groups, by="sample") %>%
group_by(mgi_symbol, group, cond, time) %>%
summarize(mean_count=mean(counts)) %>%
group_map(function(g, ...)
ggplot(g, aes(x = time, y = mean_count, fill=cond)) +
geom_bar(stat = "identity", position = position_dodge(width=0.9) ) +
scale_fill_manual(values=c("darkblue", "lightblue", "black")) +
facet_wrap(~mgi_symbol, scales = "free", ncol = 5) +
theme_bw()
)
EDIT
This is how the data looks like in the input table (after summarizing the means)
df <-
common %>%
as_tibble(rownames="gene") %>%
left_join(x= ., y = up[,1:2], by = c("gene" = "ensembl_gene_id") ) %>%
pivot_longer(starts_with("S"), names_to="sample", values_to="counts") %>%
left_join(groups, by="sample") %>%
group_by(mgi_symbol, group, cond, time) %>%
summarize(mean_count=mean(counts)) %>%
ungroup()
df
#>`summarise()` regrouping output by 'mgi_symbol', 'group', 'cond' (override with `.groups` argument)
#> # A tibble: 1,212 x 5
#> mgi_symbol group cond time mean_count
#> <chr> <int> <chr> <chr> <dbl>
#> 1 0610031O16Rik 1 WT 0h 14.4
#> 2 0610031O16Rik 2 WT 1h 30.9
#> 3 0610031O16Rik 3 WT 4h 45.5
#> 4 0610031O16Rik 4 WT 8h 56.0
#> 5 0610031O16Rik 5 GCN2-KO 0h 18.9
#> 6 0610031O16Rik 6 GCN2-KO 1h 39.4
#> 7 0610031O16Rik 7 GCN2-KO 4h 13.9
#> 8 0610031O16Rik 8 GCN2-KO 8h 13.3
#> 9 0610031O16Rik 9 GCN1-KO 0h 12.3
#> 10 0610031O16Rik 10 GCN1-KO 1h 25.3
#> # … with 1,202 more rows
Start with some dummy data. This is the data after you've finished running left_join, pivot_longer, group_by, summarize.
library(tidyverse)
df <- tibble(
time = 1:5,
mean_count = 1:5,
cond = "x"
) %>%
expand_grid(mgi_symbol = c(letters, LETTERS))
Create a column group which represents what page the mgi_symbol belongs on.
plots_per_page <- 20
df <-
df %>%
mutate(group = (dense_rank(mgi_symbol) - 1) %/% plots_per_page)
Create all the plots with group_map.
plots <-
df %>%
group_by(group) %>%
group_map(function(g, ...) {
ggplot(g, aes(x = time, y = mean_count, fill=cond)) +
geom_bar(stat = "identity", position = position_dodge(width=0.9) ) +
scale_fill_manual(values=c("darkblue", "lightblue", "black")) +
facet_wrap(~mgi_symbol, scales = "free", ncol = 5) +
theme_bw()
})
Save as multiple pages using ggpubr
ggpubr::ggexport(
ggpubr::ggarrange(plotlist = plots, nrow = 1, ncol = 1),
filename = "plots.pdf"
)

Dygraphs in R: Plot Ribbon and mean line of different groups

I recently started working dygraphs in R, and wanted to achieve a ribbon line plot with it.
Currently, I have the below ggplot which displays a ribbon (for data from multiple batches over time) and its median for two groups. Below is the code for it.
ggplot(df,
aes(x=variable, y=A, color=`[category]`, fill = `[category]`)) +
stat_summary(geom = "ribbon", alpha = 0.35) +
stat_summary(geom = "line", size = 0.9) +
theme_minimal()+ labs(x="TimeStamp")
I could add the median solid line on the dygraph, but I'm unable to add the ribbon to it. Below is the dygraph and my code for it.
df_Medians<- df%>%
group_by(variable,`[category]`) %>%
summarise(A = median(A[!is.na(A)]))
median <- cbind(as.ts(df_Medians$A))
dygraph(median) %>%
dyRangeSelector()
Is there anyway to plot something similar to the above ggplot on dygraphs? Thanks in advance.
See if the following serves your purpose:
ggplot code (for mean, replace median_se with mean_se in the stat_summary layers):
library(ggplot2)
ggplot(df,
aes(x=variable, y=A, color=category, fill = category)) +
stat_summary(geom = "ribbon", alpha = 0.35, fun.data = median_se) +
stat_summary(geom = "line", size = 0.9, fun.data = median_se) +
theme_minimal()
dygraph code (for mean, replace median_se with mean_se in the summarise step):
library(dplyr)
library(dygraph)
# calculate summary statistics for each category, & spread results out such that each row
# corresponds to one position on the x-axis
df_dygraph <- df %>%
group_by(variable, category) %>%
summarise(data = list(median_se(A))) %>%
ungroup() %>%
tidyr::unnest(data) %>%
mutate(category = as.integer(factor(category))) %>% # optional: standardizes the column
# names for summary stats
tidyr::pivot_wider(id_cols = variable, names_from = category,
values_from = c(ymin, y, ymax))
> head(df_dygraph)
# A tibble: 6 x 7
variable ymin_1 ymin_2 y_1 y_2 ymax_1 ymax_2
<int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 1 3817. 2712. 4560. 2918. 5304. 3125.
2 2 3848. 2712. 4564. 2918. 5279. 3125.
3 3 3847. 2826. 4564 2961 5281. 3096.
4 4 3722. 2827. 4331 2962. 4940. 3098.
5 5 3833. 2831. 4570. 2963 5306. 3095.
6 6 3835. 2831. 4572 2964 5309. 3097.
dygraph(df_dygraph, main = "Dygraph title") %>%
dySeries(c("ymin_1", "y_1", "ymax_1"), label = "Category 1") %>%
dySeries(c("ymin_2", "y_2", "ymax_2"), label = "Category 2") %>%
dyRangeSelector()
Code for median counterpart of mean_se:
median_se <- function(x) {
x <- na.omit(x)
se <- sqrt(var(x) / length(x))
med <- median(x)
ggplot2:::new_data_frame(list(y = med,
ymin = med - se,
ymax = med + se),
n = 1)
}
Sample data:
df <- diamonds %>%
select(price, cut) %>%
filter(cut %in% c("Fair", "Ideal")) %>%
group_by(cut) %>%
slice(1:1000) %>%
mutate(variable = rep(seq(1, 50), times = 20)) %>%
ungroup() %>%
rename(A = price, category = cut)

How to change markers on time series with plotly?

I have a dataframe containing time series data, formed by 3 columns. time, variable and category. I want to plot the time in the x axis and the variable in the y axis, and I want to make groups based on category. Additionally, I would like to modify the default markers created by plotly, so they display a rounded value of the variable.
Consider the following example:
var = rnorm(150)
var[51:100] = var[51:100] +5
var[101:150] = var[101:150] +10
time = seq(as.Date('2018-01-01'), as.Date('2018-01-01')+49, by = 'days')
df = tibble(var = var,
time = rep(time, 3),
category = c(rep('a', 50), rep('b', 50), rep('c', 50)))
head(df)
var time category
<dbl> <date> <chr>
1 0.330 2018-01-01 a
2 -0.786 2018-01-02 a
3 -0.838 2018-01-03 a
4 -0.0719 2018-01-04 a
5 0.0320 2018-01-05 a
6 -1.16 2018-01-06 a
library(plotly)
df %>% group_by(category) %>%
plot_ly(x = ~ time, y = ~ var, color = ~ category, mode = 'lines+markers')
This generates the kind of plot that I want: see here, but when I try to modify the the markers:
df %>% group_by(category) %>%
plot_ly(x = ~ time, y = ~ var, color = ~ category, mode = 'lines+markers') %>%
add_markers(text = ~ paste("<b>Variable:</b> ", round(var, 2),
"<br />",
"<b>Time:</b> ", time), hoverinfo = "text")
It transforms the plot drawing just the dots but not the lines.see here. If I try to force adding the lines with the command add_lines() then I have a double legend, with values for the dots and the lines separatedly.
df %>% group_by(category) %>%
plot_ly(x = ~ time, y = ~ var, color = ~ category, mode = 'lines+markers') %>%
add_markers(text = ~ paste("<b>Variable:</b> ", round(var, 2),
"<br />",
"<b>Time:</b> ", time), hoverinfo = "text") %>%
add_lines()
Is there a way to plot a time series with plotly that includes lines, and customized markers? Im sorry if this is a silly question, I am quite new to plotly.
If you want one trace with both markers and lines then stick with the plot_ly function instead of adding traces. Try this:
library(plotly)
df %>%
group_by(category) %>%
plot_ly(x = ~ time, y = ~ var, color = ~ category, mode = 'lines+markers', type = "scatter",
text = ~ paste("<b>Variable:</b> ", round(var, 2),
"<br />",
"<b>Time:</b> ", time), hoverinfo = "text")

Barplot Indicating the statistically significant difference

I need to draw a bar plot for significant SNP codes (categorical) against the corresponding phenotype, similar to these plots:
I tried many ways in R and got some results but I field to got my favorite result. Here are the codes and results:
### DATA
SNP_code <- as.factor(c("GG","GA","AA","GA","GA","GG","GG","GG","GG","GA","GA","AA","GA","GA","GA","GG","GG","GG","GG","AA","GG","GG","GG","GG","AA","GG","GG","GA","GG","AA","GA","GG","GG","GG","GG","GG","GG","AA","GG","GA","GG","GG","GA","GG","GG","GA","GG","GG","GA","GA","GG","GA","GG","GA","GA","GA","GA","GA","GA","GG","GG","GG","AA","GA","GA","GA","GA","GG","GA","GG","GG","GG","GA","GA","GA","GG","GG","GA","GG","AA","GG","GG","GG","AA"))
EBV <- c(0.06663,-0.03031,-0.122,-0.02021,-0.1157,-0.08131,-0.02034,-0.06324,0.06699,-0.062,0.02736,-0.1201,-0.04846,-0.06934,-0.06023,-0.009244,-0.05648,-0.01908,0.06728,-0.06517,0.08534,0.07618,-0.0814,0.06113,-0.0795,0.1055,0.08305,0.1209,-0.05314,-0.09431,0.05185,0.1347,0.1591,0.08777,0.08326,0.1612,0.09528,-0.1002,0.1561,-0.09327,0.09474,0.1356,0.06384,0.1585,0.03235,0.1081,0.1462,-0.04082,-0.05042,0.01793,-0.1157,-0.1165,-0.009399,-0.02311,-0.108,-0.1143,0.07219,0.01376,-0.05059,-0.052,0.08494,-0.0388,-0.06346,0.07789,0.02961,-0.1126,0.1102,0.133,-0.09317,-0.1181,0.1584,0.122,0.1019,-0.04074,-0.01178,0.09523,-0.03266,-0.01258,-0.0231,-0.08259,0.05823,-0.02894,-0.008242,0.07981)
LS <- c(2,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,1,2,2,2,1,1,1,2,2,2,2,2,1,1,2,1,2,2,2,1,2,2,2,1,1,2,1,1,1,1,1,1,1,1,1,1,2,1,1,2,1,1,2,2,1,1,2,1,2,1,1,2,1,1,1,1,1,1,1,2)
IDs <- c(1033,1081,1106,1107,1120,1194,1199,1326,1334,1340,1345,1358,1398,1404,1405,1421,1457,1459,1464,1509,1529,1542,1550,2025,2030,2095,2099,2128,2141,2153,2167,2224,2232,2238,2244,2266,2271,2280,2283,2323,2326,2337,2369,2390,2391,2396,851012,851016,851021,851055,851063,851084,851105,851109,851146,851169,851176,851198,851205,851246,851266,851292,851332,851345,851488,851489,851509,851528,851531,851547,851562,851573,851574,851578,851584,851588,851592,851622,851651,851670,851672,851684,851690,861086)
sig_snp <- data.frame(IDs, SNP_code, EBV, LS)
### Variance analysis and Mean comparison
library(dplyr)
### for LS
group_by(sig_snp, SNP_code) %>%
summarise(
count = n(),
mean = mean(LS, na.rm = TRUE),
sd = sd(LS, na.rm = TRUE))
### for EBV
group_by(sig_snp, SNP_code) %>%
summarise(
count = n(),
mean = mean(EBV, na.rm = TRUE),
sd = sd(EBV, na.rm = TRUE))
# Compute the analysis of variance
Anova.fit <- aov(EBV ~ SNP_code, data = sig_snp)
summary(Anova.fit)
# Tukey multiple pairwise-comparisons
TukeyHSD(Anova.fit)
# or
library(multcomp)
summary(glht(Anova.fit, linfct = mcp(SNP_code = "Tukey")))
### Box plot for EBV (actually I need Barplot for LS and EBV)
library(ggplot2)
library(ggpval)
plot <- ggplot(sig_snp, aes(SNP_code, EBV)) +
geom_boxplot(fill=c("red","blue", "green"), color="black", width=.7); plot
add_pval(plot, pairs = list(c(1, 3)), test='wilcox.test')
add_pval(plot, pairs = list(c(2, 3)), test='wilcox.test')
add_pval(plot, pairs = list(c(1, 2)), test='wilcox.test')
"add_pval" only use "wilcox.test" and "t.test", but I perfer Tukey.
Any help is appreciated.
There is definitely room for improvement of the code that I posted below, but at least it gives you one example of the workflow you can use for getting your "favorite" barplot:
Part A: Barchart
1) We re-organise sig_snp in order to get a dataframe with the mean of each SNP in function of EBV or LS.
library(tidyverse)
DF1 <- sig_snp %>%
pivot_longer(., cols = c(EBV,LS), names_to = "Variable", values_to = "Values") %>%
group_by(SNP_code, Variable) %>%
summarise(Mean = mean(Values),
SEM = sd(Values) / sqrt(n()),
Nb = n()) %>%
rowwise() %>%
mutate(Labels = as.character(SNP_code)) %>%
mutate(Labels = paste(unlist(strsplit(Labels,"")),collapse = "/")) %>%
mutate(Labels = paste0(Labels,"\nn = ",Nb))
# A tibble: 6 x 6
SNP_code Variable Mean SEM Nb Labels
<fct> <chr> <dbl> <dbl> <int> <chr>
1 AA EBV -0.0719 0.0202 9 "A/A\nn = 9"
2 AA LS 1.11 0.111 9 "A/A\nn = 9"
3 GA EBV -0.0141 0.0134 31 "G/A\nn = 31"
4 GA LS 1.23 0.0763 31 "G/A\nn = 31"
5 GG EBV 0.0422 0.0126 44 "G/G\nn = 44"
6 GG LS 1.48 0.0762 44 "G/G\nn = 44"
The labels column will be re-used later for the labeling of x-axis.
2) Then, we are going to calculate the total mean (that will hep to draw the "Mean" bar) by doing:
library(tidyverse)
DF2 <- sig_snp %>%
pivot_longer(., cols = c(EBV,LS), names_to = "Variable", values_to = "Values") %>%
group_by(Variable) %>%
summarise(Mean = mean(Values),
SEM = sd(Values) / sqrt(n()),
Nb = n()) %>%
mutate(SNP_code = "All") %>%
select(SNP_code, Variable, Mean, SEM, Nb) %>%
rowwise() %>%
mutate(Labels = paste0("Mean\nn = ",Nb))
# A tibble: 2 x 6
SNP_code Variable Mean SEM Nb Labels
<chr> <chr> <dbl> <dbl> <int> <chr>
1 All EBV 0.00918 0.00944 84 "Mean\nn = 84"
2 All LS 1.35 0.0522 84 "Mean\nn = 84"
3) we are binding both DF1 and DF2 and we re-organize the levels of SNP_code in order to get the correct plotting order:
library(tidyverse)
DF <- bind_rows(DF1, DF2)
DF$Labels = factor(DF$Labels,levels= c("Mean\nn = 84",
"A/A\nn = 9",
"G/A\nn = 31",
"G/G\nn = 44" ))
4) Now, we can plot it:
library(ggplot2)
ggplot(DF, aes(x = SNP_code, y = Mean, fill = SNP_code))+
geom_bar(stat = "identity", show.legend = FALSE)+
geom_errorbar(aes(ymin = Mean-SEM, ymax = Mean+SEM), width = 0.2)+
facet_wrap(.~Variable, scales = "free")+
scale_x_discrete(name = "",labels = levels(DF$Labels))
Part B: Adding statistic on the barchart
For adding statistic, you can have the use of geom_signif function from ggsignif package that allow to add statistics from an external output.
1) First create the dataframe for the output of Tukey test on EBV:
Anova.fit <- aov(EBV ~ SNP_code, data = sig_snp)
t <- TukeyHSD(Anova.fit)
stat <- t$SNP_code
Stat_EBV <- stat %>% as.data.frame() %>%
mutate(Variable = "EBV") %>%
mutate(Group = rownames(stat)) %>%
rowwise() %>%
mutate(Group1 = unlist(strsplit(Group,"-"))[1]) %>%
mutate(Group2 = unlist(strsplit(Group,"-"))[2]) %>%
mutate(labels = round(`p adj`,4))
Stat_EBV$y_pos <- c(0.06,0.08,0.1)
2) same thing for the Tukey test of LS:
Anova.fit <- aov(LS ~ SNP_code, data = sig_snp)
t <- TukeyHSD(Anova.fit)
stat <- t$SNP_code
Stat_LS <- stat %>% as.data.frame() %>%
mutate(Variable = "LS") %>%
mutate(Group = rownames(stat)) %>%
rowwise() %>%
mutate(Group1 = unlist(strsplit(Group,"-"))[1]) %>%
mutate(Group2 = unlist(strsplit(Group,"-"))[2]) %>%
mutate(labels = round(`p adj`,4))
Stat_LS$y_pos = c(1.7,1.9,2.1)
3) Binding of both stats dataframes:
library(tidyverse)
STAT <- bind_rows(Stat_EBV,Stat_LS)
# A tibble: 6 x 10
diff lwr upr `p adj` Variable Group Group1 Group2 labels y_pos
<dbl> <dbl> <dbl> <dbl> <chr> <chr> <chr> <chr> <dbl> <dbl>
1 0.0578 -0.0130 0.129 0.132 EBV GA-AA GA AA 0.132 0.06
2 0.114 0.0457 0.183 0.000431 EBV GG-AA GG AA 0.0004 0.08
3 0.0563 0.0125 0.100 0.00821 EBV GG-GA GG GA 0.0082 0.1
4 0.115 -0.303 0.532 0.790 LS GA-AA GA AA 0.790 1.7
5 0.366 -0.0373 0.770 0.0832 LS GG-AA GG AA 0.0832 1.9
6 0.251 -0.00716 0.510 0.0585 LS GG-GA GG GA 0.0585 2.1
4) Get the barchart and add the statistic results:
library(ggplot2)
library(ggsignif)
ggplot(DF, aes(x = SNP_code, y = Mean, fill = SNP_code))+
geom_bar(stat = "identity", show.legend = FALSE)+
geom_errorbar(aes(ymin = Mean-SEM, ymax = Mean+SEM), width = 0.2)+
geom_signif(inherit.aes = FALSE, data = STAT,
aes(xmin=Group1, xmax=Group2, annotations=labels, y_position=y_pos),
manual = TRUE)+
facet_wrap(.~Variable, scales = "free")+
scale_x_discrete(name = "",labels = levels(DF$Labels))
I hope it looks what you are expecting.

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