How to extract stat_smooth curve maxima in gpplot panel (facet_grid)? - ggplot2

I have created this plot with 18 grids using facet_grid command and two different fitting equations (for Jan - Apr, and May - Jun). I have two things that I need help with:
(may sound obvious, but) I haven't been able to find on the internet working codes extract a curve maximum for a stat_smooth fit. I'd appreciate if someone could show and explain what the codes mean. This is the closest I could find, but I am not sure what it means:
gb <- ggplot_build(p1)
curve_max <- gb$data[[1]]$x[which(diff(sign(diff(gb$data[[1]]$y)))==-2)+1]
How to add a vertical line to indicate max value on each curve?
Data file (rlc2 <- read_excel)
Plot
plot <- ggplot(rlc2, aes(par, etr, color=month, group=site))+
geom_point()+
stat_smooth(data = subset(rlc2, rlc2$month!="May" & rlc2$month!="Jun"),
method = "glm",
formula = y ~ x + log(x),
se = FALSE,
method.args = list(family = gaussian(link = "log"), start=c(a=0, b=0, c=0)))+
stat_smooth(data = subset(rlc2, rlc2$month=="May" | rlc2$month=="Jun"),
method = "nlsLM",
formula = y ~ M*(1 - exp(-(a*x))),
se = FALSE,
method.args = list(start=c(M=0, a=10)))+
facet_grid(rows = vars(month), cols = vars(site))
plot
field_rlc_plot
Any other advice are also welcome. I am educated as programmer so my codes are probably a bit messy. Thank you for helping.

Try this:
First, fit the data and extract the maximum of the fit.
my.fit <- function(month, site, data) {
fit <- glm(formula = etr ~ par + log(par),
data = data,
family=gaussian(link = "log")
)
#arrange the dersired output in a tibble
tibble(max = max(fit$fitted.values),
site = site,
month = month)
}
#Apply a custom function `my.fit` on each subset of data
#according to month and site using the group_by/nest/map method
# the results are rowbinded and returned in a data.frame
my.max<-
rlc2 %>%
dplyr::group_by(month, site) %>%
tidyr::nest() %>%
purrr::pmap_dfr(my.fit)
Next, join the results back on your data and plot a geom_line
rlc2 %>%
dplyr::left_join(my.max) %>%
ggplot(aes(x = par, y = etr))+
geom_point()+
stat_smooth(data = subset(rlc2, rlc2$month!="May" & rlc2$month!="Jun"),
method = "glm",
formula = y ~ x + log(x),
se = FALSE,
method.args = list(family = gaussian(link = "log"), start=c(a=0, b=0, c=0)))+
stat_smooth(data = subset(rlc2, rlc2$month=="May" | rlc2$month=="Jun"),
method = "nlsLM",
formula = y ~ M*(1 - exp(-(a*x))),
se = FALSE,
method.args = list(start=c(M=0, a=10)))+
geom_line(aes(y=max), col="red")+
facet_grid(rows = vars(month), cols = vars(site))

Related

plot gam results with original x values (not scaled and centred)

I have a dataset that I am modeling with a gam. Because there are two continuous varaibles in the gam, I have centred and scaled these variables before adding them to the model. Therefore, when I use the built-in features in gratia to show the results, the x values are not the same as the original scale. I'd like to plot the results using the scale of the original data.
An example:
library(tidyverse)
library(mgcv)
library(gratia)
set.seed(42)
df <- data.frame(
doy = sample.int(90, 300, replace = TRUE),
year = sample(c(1980:2020), size = 300, replace = TRUE),
site = c(rep("A", 150), rep("B", 80), rep("C", 70)),
sex = sample(c("F", "M"), size = 300, replace = TRUE),
mass = rnorm(300, mean = 500, sd = 50)) %>%
mutate(doy.s = scale(doy, center = TRUE, scale = TRUE),
year.s = scale(year, center = TRUE, scale = TRUE),
across(c(sex, site), as.factor))
m1 <- gam(mass ~
s(year.s, site, bs = "fs", by = sex, k = 5) +
s(doy.s, site, bs = "fs", by = sex, k = 5) +
s(sex, bs = "re"),
data = df, method = "REML", family = gaussian)
draw(m1)
How do I re-plot the last two panels in this figure to show the relationship between year and mass with ggplot?
You can't do this with gratia::draw automatically (unless I'm mistaken).* But you can use gratia::smooth_estimates to get a dataframe which you can then do whatever you like with.
To answer your specific question: to re-plot the last two panels of the plot you provided, but with year unscaled, you can do the following
# Get a tibble of smooth estimates from the model
sm <- gratia::smooth_estimates(m1)
# Add a new column for the unscaled year
sm <- sm %>% mutate(year = mean(df$year) + (year.s * sd(df$year)))
# Plot the smooth s(year.s,site) for sex=F with year unscaled
pF <- sm %>% filter(smooth == "s(year.s,site):sexF" ) %>%
ggplot(aes(x = year, y = est, color=site)) +
geom_line() +
theme(legend.position = "none") +
labs(y = "Partial effect", title = "s(year.s,site)", subtitle = "By: sex; F")
# Plot the smooth s(year.s,site) for sex=M with year unscaled
pM <- sm %>% filter(smooth == "s(year.s,site):sexM" ) %>%
ggplot(aes(x = year, y = est, color=site)) +
geom_line() +
theme(legend.position = "none") +
labs(y = "Partial effect", title = "s(year.s,site)", subtitle = "By: sex; M")
library(patchwork) # use `patchwork` just for easy side-by-side plots
pF + pM
to get:
EDIT: If you also want to shift result on the y-axis as #GavinSimpson (who is the author and maintainer of gratia) mentioned, you can do this with add_constant, adding this code before plotting above:
sm <- sm %>%
add_constant(coef(m1)["(Intercept)"]) %>%
transform_fun(inv_link(m1))
[You should also in general untransform the smooth by the inverse of the model's link function. In your case this is just the identity, so it is not necessary, but in general it would be. That's what the second step above is doing.]
In your example, this results in:
*As mentioned in the custom-plotting vignette for gratia, the goal of draw not to be fully customizable, but just to be useful default. See there for recommendations about custom plots.

Adding stat = count on top of histogram in ggplot

I've seen some other examples (especially using geom_col() and stat_bin()) to add frequency or count numbers on top of bars. I'm trying to get this to work with geom_histogram() where I have a discrete (string), not continuous, x variable.
library(tidyverse)
d <- cars |>
mutate( discrete_var = factor(speed))
ggplot(d, aes(x = discrete_var)) +
geom_histogram(stat = "count") +
stat_bin(binwidth=1, geom='text', color='white', aes(label=..count..),
position=position_stack(vjust = 0.5)) +
Gives me an error because StatBin requires a continuous x variable. Any quick fix ideas?
The error message gives you the answer: ! StatBin requires a continuous x variable: the x variable is discrete.Perhaps you want stat="count"?
So instead of stat_bin() use stat_count()
And for further reference here is a reproducible example:
library(tidyverse)
d <- cars |>
mutate( discrete_var = factor(speed))
ggplot(data = d,
aes(x = discrete_var)) +
geom_histogram(stat = "count") +
stat_count(binwidth = 1,
geom = 'text',
color = 'white',
aes(label = ..count..),
position = position_stack(vjust = 0.5))

Adding percentage labels to a barplot with y-axis 'count' in R

I'd like to add percentage labels per gear to the bars but keep the count y-scale.
E.g. 10% of all 'gear 3' are '4 cyl'
library(ggplot)
ds <- mtcars
ds$gear <- as.factor(ds$gear)
p1 <- ggplot(ds, aes(gear, fill=gear)) +
geom_bar() +
facet_grid(cols = vars(cyl), margins=T)
p1
Ideally only in ggplot, wihtout adding dplyr or tidy. I found some of these solutions but then I get other issues with my original data.
EDIT: Suggestions that this is a duplicate from:
enter link description here
I saw this also earlier, but wasn't able to integrate that code into what I want:
# i just copy paste some of the code bits and try to reconstruct what I had earlier
ggplot(ds, aes(gear, fill=gear)) +
facet_grid(cols = vars(cyl), margins=T) +
# ..prop.. meaning %, but i want to keep the y-axis as count
geom_bar(aes(y = ..prop.., fill = factor(..x..)), stat="count") +
# not sure why, but I only get 100%
geom_text(aes( label = scales::percent(..prop..),
y= ..prop.. ), stat= "count", vjust = -.5)
The issue is that ggplot doesn't know that each facet is one group. This very useful tutorial helps with a nice solution. Just add aes(group = 1)
P.S. At the beginning, I was often quite reluctant and feared myself to manipulate my data and pre-calculate data frames for plotting. But there is no need to fret! It is actually often much easier (and safer!) to first shape / aggregate your data into the right form and then plot/ analyse the new data.
library(tidyverse)
library(scales)
ds <- mtcars
ds$gear <- as.factor(ds$gear)
First solution:
ggplot(ds, aes(gear, fill = gear)) +
geom_bar() +
facet_grid(cols = vars(cyl), margins = T) +
geom_text(aes(label = scales::percent(..prop..), group = 1), stat= "count")
edit to reply to comment
Showing percentages across facets is quite confusing to the reader of the figure and I would probably recommend against such a visualization. You won't get around data manipulation here. The challenge is here to include your "facet margin". I create two summary data frames and bind them together.
ds_count <-
ds %>%
count(cyl, gear) %>%
group_by(gear) %>%
mutate(perc = n/sum(n)) %>%
ungroup %>%
mutate(cyl = as.character(cyl))
ds_all <-
ds %>%
count(cyl, gear) %>%
group_by(gear) %>%
summarise(n = sum(n)) %>%
mutate(cyl = 'all', perc = 1)
ds_new <- bind_rows(ds_count, ds_all)
ggplot(ds_new, aes(gear, fill = gear)) +
geom_col(aes(gear, n, fill = gear)) +
facet_grid(cols = vars(cyl)) +
geom_text(aes(label = scales::percent(perc)), stat= "count")
IMO, a better way would be to simply swap x and facetting variables. Then you can use ggplots summarising function as above.
ggplot(ds, aes(as.character(cyl), fill = gear)) +
geom_bar() +
facet_grid(cols = vars(gear), margins = T) +
geom_text(aes(label = scales::percent(..prop..), group = 1), stat= "count")
Created on 2020-02-07 by the reprex package (v0.3.0)

Error while finding topics quantity on Latent Dirichlet Allocation model using ldatuning library

This is the outcome error and I can tell this is because there is at least one document without some term, but I don't get why and how I can solve it.
prep_fun = function(x) {
x %>%
str_to_lower %>% #make text lower case
str_replace_all("[^[:alpha:]]", " ") %>% #remove non-alpha symbols - chao punctuation y #
str_replace_all("\\s+", " ") %>% #collapse multiple spaces
str_replace_all("\\W*\\b\\w\\b\\W*", " ") #Remuevo letras individuales
}
tok_fun <- function(x) {
tokens <- word_tokenizer(x)
textstem::lemmatize_words(tokens)
}
it_patentes <- itoken(data$Abstract,
preprocessor = prep_fun,
tokenizer = tok_fun,
ids = data$id,
progressbar = F)
vocab <- create_vocabulary(it_patentes, ngram = c(ngram_min = 1L, ngram_max = 3L),
stopwords = tm::stopwords("english"))
pruned_vocab <- prune_vocabulary(vocab, term_count_min = max(vocab$term_count)*.01,
doc_proportion_min = 0.001)
vectorizer <- vocab_vectorizer(pruned_vocab)
dtm <- create_dtm(it_patentes, vectorizer,type = "dgTMatrix", progressbar = FALSE)
> #Plot the metrics to get number of topics
> t1 <- Sys.time()
> tunes <- FindTopicsNumber(
+ dtm = dtm,
+ topics = c(2:25),
+ metrics = c("Griffiths2004", "CaoJuan2009", "Arun2010"),
+ method = "Gibbs",
+ control = list(seed = 17),
+ mc.cores = 4L,
+ verbose = TRUE
+ )
fit models...Error in checkForRemoteErrors(val) :
4 nodes produced errors; first error: Each row of the input matrix needs to contain at least one non-zero entry
> print(difftime(Sys.time(), t1, units = 'sec'))
Time difference of 9.155343 secs
> FindTopicsNumber_plot(tunes)
Error in base::subset(values, select = 2:ncol(values)) :
object 'tunes' not found
Even though I know ldatuning is made for topicmodels, I don't think there might be a huge difference to get a number to start testing, is there?
ldatuning expects input dtm matrix in a different format (format from topicmodels package). You need to convert dtm (sparse matrix from Matrix package) to a format which ldatuning can understand

Depth Profiling visualization

I'm trying to create a depth profile graph with the variables depth, distance and temperature. The data collected is from 9 different points with known distances between them (distance 5m apart, 9 stations, 9 different sets of data). The temperature readings are according to these 9 stations where a sonde was dropped directly down, taking readings of temperature every 2 seconds. Max depth at each of the 9 stations were taken from the boat also.
So the data I have is:
Depth at each of the 9 stations (y axis)
Temperature readings at each of the 9 stations, at around .2m intervals vertical until the bottom was reached (fill area)
distance between the stations, (x axis)
Is it possible to create a depth profile similar to this? (obviously without the greater resolution in this graph)
I've already tried messing around with ggplot2 and raster but I just can't seem to figure out how to do this.
One of the problems I've come across is how to make ggplot2 distinguish between say 5m depth temperature reading at station 1 and 5m temperature reading at station 5 since they have the same depth value.
Even if you can guide me towards another program that would allow me to create a graph like this, that would be great
[ REVISION ]
(Please comment me if you know more suitable interpolation methods, especially not needing to cut under bottoms data.)
ggplot() needs long data form.
library(ggplot2)
# example data
max.depths <- c(1.1, 4, 4.7, 7.7, 8.2, 7.8, 10.7, 12.1, 14.3)
depth.list <- sapply(max.depths, function(x) seq(0, x, 0.2))
temp.list <- list()
set.seed(1); for(i in 1:9) temp.list[[i]] <- sapply(depth.list[[i]], function(x) rnorm(1, 20 - x*0.5, 0.2))
set.seed(1); dist <- c(0, sapply(seq(5, 40, 5), function(x) rnorm(1, x, 1)))
dist.list <- sapply(1:9, function(x) rep(dist[x], length(depth.list[[x]])))
main.df <- data.frame(dist = unlist(dist.list), depth = unlist(depth.list) * -1, temp = unlist(temp.list))
# a raw graph
ggplot(main.df, aes(x = dist, y = depth, z = temp)) +
geom_point(aes(colour = temp), size = 1) +
scale_colour_gradientn(colours = topo.colors(10))
# a relatively raw graph (don't run with this example data)
ggplot(main.df, aes(x = dist, y = depth, z = temp)) +
geom_raster(aes(fill = temp)) + # geom_contour() +
scale_fill_gradientn(colours = topo.colors(10))
If you want a graph such like you showed, you have to do interpolation. Some packages give you spatial interpolation methods. In this example, I used akima package but you should think seriously that which interpolation methods to use.
I used nx = 300 and ny = 300 in below code but I think it would be better to decide those values carefully. Large nx and ny gives a high resolution graph, but don't foreget real nx and ny (in this example, real nx is only 9 and ny is 101).
library(akima); library(dplyr)
interp.data <- interp(main.df$dist, main.df$depth, main.df$temp, nx = 300, ny = 300)
interp.df <- interp.data %>% interp2xyz() %>% as.data.frame()
names(interp.df) <- c("dist", "depth", "temp")
# draw interp.df
ggplot(interp.df, aes(x = dist, y = depth, z = temp)) +
geom_raster(aes(fill = temp)) + # geom_contour() +
scale_fill_gradientn(colours = topo.colors(10))
# to think appropriateness of interpolation (raw and interpolation data)
ggplot(interp.df, aes(x = dist, y = depth, z = temp)) +
geom_raster(aes(fill = temp), alpha = 0.3) + # interpolation
scale_fill_gradientn(colours = topo.colors(10)) +
geom_point(data = main.df, aes(colour = temp), size = 1) + # raw
scale_colour_gradientn(colours = topo.colors(10))
Bottoms don't match !!I found ?interp says "interpolation only within convex hull!", oops... I'm worrid about the interpolation around the problem-area, is it OK ? If no problem, you need only cut the data under the bottoms. If not, ... I can't answer immediately (below is an example code to cut).
bottoms <- max.depths * -1
# calculate bottom values using linear interpolation
approx.bottoms <- approx(dist, bottoms, n = 300) # n must be the same value as interp()'s nx
# change temp values under bottom into NA
library(dplyr)
interp.cut.df <- interp.df %>% cbind(bottoms = approx.bottoms$y) %>%
mutate(temp = ifelse(depth >= bottoms, temp, NA)) %>% select(-bottoms)
ggplot(interp.cut.df, aes(x = dist, y = depth, z = temp)) +
geom_raster(aes(fill = temp)) +
scale_fill_gradientn(colours = topo.colors(10)) +
geom_point(data = main.df, size = 1)
If you want to use stat_contour
It is harder to use stat_contour than geom_raster because it needs a regular grid form. As far as I see your graph, your data (depth and distance) don't form a regular grid, it means it is much difficult to use stat_contour with your raw data. So I used interp.cut.df to draw a contour plot. And stat_contour have a endemic problem (see How to fill in the contour fully using stat_contour), so you need to expand your data.
library(dplyr)
# 1st: change NA into a temp's out range value (I used 0)
interp.contour.df <- interp.cut.df
interp.contour.df[is.na(interp.contour.df)] <- 0
# 2nd: expand the df (It's a little complex, so please use this function)
contour.support.func <- function(df) {
colname <- names(df)
names(df) <- c("x", "y", "z")
Range <- as.data.frame(sapply(df, range))
Dim <- as.data.frame(t(sapply(df, function(x) length(unique(x)))))
arb_z = Range$z[1] - diff(Range$z)/20
df2 <- rbind(df,
expand.grid(x = c(Range$x[1] - diff(Range$x)/20, Range$x[2] + diff(Range$x)/20),
y = seq(Range$y[1], Range$y[2], length = Dim$y), z = arb_z),
expand.grid(x = seq(Range$x[1], Range$x[2], length = Dim$x),
y = c(Range$y[1] - diff(Range$y)/20, Range$y[2] + diff(Range$y)/20), z = arb_z))
names(df2) <- colname
return(df2)
}
interp.contour.df2 <- contour.support.func(interp.contour.df)
# 3rd: check the temp range (these values are used to define contour's border (breaks))
range(interp.cut.df$temp, na.rm=T) # 12.51622 20.18904
# 4th: draw ... the bottom border is dirty !!
ggplot(interp.contour.df2, aes(x = dist, y = depth, z = temp)) +
stat_contour(geom="polygon", breaks = seq(12.51622, 20.18904, length = 11), aes(fill = ..level..)) +
coord_cartesian(xlim = range(dist), ylim = range(bottoms), expand = F) + # cut expanded area
scale_fill_gradientn(colours = topo.colors(10)) # breaks's length is 11, so 10 colors are needed
# [Note]
# You can define the contour's border values (breaks) and colors.
contour.breaks <- c(12.5, 13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5, 20.5)
# = seq(12.5, 20.5, 1) or seq(12.5, 20.5, length = 9)
contour.colors <- c("darkblue", "cyan3", "cyan1", "green3", "green", "yellow2","pink", "darkred")
# breaks's length is 9, so 8 colors are needed.
# 5th: vanish the bottom border by bottom line
approx.df <- data.frame(dist = approx.bottoms$x, depth = approx.bottoms$y, temp = 0) # 0 is dummy value
ggplot(interp.contour.df2, aes(x = dist, y = depth, z = temp)) +
stat_contour(geom="polygon", breaks = contour.breaks, aes(fill = ..level..)) +
coord_cartesian(xlim=range(dist), ylim=range(bottoms), expand = F) +
scale_fill_gradientn(colours = contour.colors) +
geom_line(data = approx.df, lwd=1.5, color="gray50")
bonus: legend technic
library(dplyr)
interp.contour.df3 <- interp.contour.df2 %>% mutate(temp2 = cut(temp, breaks = contour.breaks))
interp.contour.df3$temp2 <- factor(interp.contour.df3$temp2, levels = rev(levels(interp.contour.df3$temp2)))
ggplot(interp.contour.df3, aes(x = dist, y = depth, z = temp)) +
stat_contour(geom="polygon", breaks = contour.breaks, aes(fill = ..level..)) +
coord_cartesian(xlim=range(dist), ylim=range(bottoms), expand = F) +
scale_fill_gradientn(colours = contour.colors, guide = F) + # add guide = F
geom_line(data = approx.df, lwd=1.5, color="gray50") +
geom_point(aes(colour = temp2), pch = 15, alpha = 0) + # add
guides(colour = guide_legend(override.aes = list(colour = rev(contour.colors), alpha = 1, cex = 5))) + # add
labs(colour = "temp") # add
You want to treat this as a 3-D surface with temperature as the z dimension. The given plot is a contour plot and it looks like ggplot2 can do that with stat_contour.
I'm not sure how the contour lines are computed (often it's linear interpolation along a Delaunay triangulation). If you want more control over how to interpolate between your x/y grid points, you can calculate a surface model first and feed those z coordinates into ggplot2.