Al generar los gráficos salta error, he probado a utilizar el .csv tanto con el paso de interpolación como sin él por si fuera la causa pero el error es el mismo.

Moving Average Smoothing parameters

MA_order <- 12

Dataframe reordering for facet plotting

df_MA <- data.frame(apply(df[,c("vt","convexity", "circularity", "major","minor")], 2, SMA, n=MA_order))
df_MA <- df_MA %>% mutate_all(funs((. - min(., na.rm = T))/(max(., na.rm = T) - min(., na.rm = T))))
df_MA_long <- melt(df_MA)
Time = rep(1:181, 5)

Plot generation

Time series trajectory

p1 <- ggplot(df, aes(x=frame, y=y)) +
geom_line() +
xlab("") +
ylab("Position (microns)") +
theme_bw() +
geom_vline(xintercept = c(best.case$end, best.case$begin),
color = "black", size=0.5)

Moving average values of each morphological descriptor and velocity

p2 <- ggplot(data=df_MA_long, aes(x=Time, y=1, fill=value, color=variable)) +
facet_wrap(~variable, ncol=1, scales='free') +
scale_fill_gradientn(colours=c("#15BFC3", "#FC367A", "white", "gray"),
na.value = "transparent",
breaks=c(0,0.5,1),labels=c(0,0.5,1),
limits=c(0,1)) +
theme_bw() +
ylab('') +
geom_raster() +
labs(fill = "Relative\nvalue") +
theme(axis.text.y=element_blank(),axis.ticks.y=element_blank()) +
geom_vline(xintercept = c(best.case$end, best.case$begin),
color = "black", size=0.5)

Arranging the plots in the same column for better visualization, using egg library.

ggarrange(p1,p2, ncol = 1,heights = c(2, 4))

Error: Aesthetics must be either length 1 or the same as the data (900): x
Traceback:

1. ggarrange(p1, p2, ncol = 1, heights = c(2, 4))
2. lapply(plots, ggplot2::ggplotGrob)
3. FUN(X[[i]], ...)
4. ggplot_gtable(ggplot_build(x))
5. ggplot_build(x)
6. ggplot_build.ggplot(x)
7. by_layer(function(l, d) l$compute_aesthetics(d, plot))
8. f(l = layers[[i]], d = data[[i]])
9. l$compute_aesthetics(d, plot)
10. f(..., self = self)
11. check_aesthetics(evaled, n)
12. abort(glue("Aesthetics must be either length 1 or the same as the data ({n}): ",
    . glue_collapse(names(which(!good)), ", ", last = " and ")))
13. signal_abort(cnd)

Salta el mensaje de que no tengo FIJI instalado aunque lo tenga en la misma ruta de siempre, parece que si ejecuta el código correctamente (en este en concreto no detecta célula pero en otros las detecta igual que antes)

`jpincru@pop-os:~$ Tronos --source /home/jpincru/pelisdv/Sandra/TL1_sandra_AFA854_*_R3D.dv --workdir /home/jpincru/pelisdv/Sandra/results --project --track --threshold MaxEntropy --convert --minframes 120 --sizes 500 20000

/_ // __ \ / __ \ / | / // __ / /
/ / / // // / / // |/ // / / /_ \
/ / / , // // // /| // // // /
// // || _/// |/ _//_/

Welcome to TRONOS 0.2.0 by Daniel Leon-Perinan
[INFO] Parsing arguments...
[INFO] Z-Stacking will occur now
100%|██████████████████████████████████████████████████████| 107/107 [00:02<00:00, 37.54it/s]
[INFO] Saving projected image to .tif
[INFO] Generating and saving MaxEntropy threshold image
[TRONOS] [ERROR] Could not find FIJI installed in your Linux system
[TRONOS]->[FIJI] Passing data for file /home/jpincru/pelisdv/Sandra/results/TL1_sandra_AFA854_1_R3D_PRJ
[FIJI] Analyzing particles with default parameters
[TRONOS] [ERROR] Could not find FIJI installed in your Linux system
[FIJI]->[TRONOS] Result parsing and transformation
[TRONOS] Trajectory linking
[TRONOS] Filtering trajectories
[TRONOS] Track filter statistics
Before: 1
After: 0
[TRONOS] Trajectories were successfully saved to file /home/jpincru/pelisdv/Sandra/results/TL1_sandra_AFA854_1_R3D_PRJ_trajs.csv
[INFO] Completed processing of TL1_sandra_AFA854_1_R3D
`

Al cambiar la ruta del output para el pdf da error, solo se genera correctamente en la carpeta del notebook si se deja por defecto.

Calculate the global spectrum and plot

y.spec <- spectrum(y,log="yes",span=2,plot=FALSE,na.action=na.remove)

​

Axis readjustment

spx <- y.spec$freq/sampling.time

spy <- 2*y.spec$spec

​

p.freq <- ggplot(data.frame(spy, spx), aes(y = spy, x = spx)) +

   geom_line() +

   theme_bw() +

   ggtitle(label = "Nuclear oscillations frequencies") +

   xlab("Frequency (Hz)") +

   ylab("Spectral density")

​

p.period <- ggplot(data.frame(spy, spx), aes((1/spx)/60, spy)) +

   geom_line() +

   ggtitle(label = "Nuclear oscillations periods") +

   theme_bw() +

   ylab("Spectral density") + 

   scale_x_continuous(trans = "log10") +

   xlab("Period (minutes)")

​

p.freq

p.period

​

pdf(paste0(analysis.name,"home/jpincru/pelisdv/pdfs/density/_spectral_density.pdf"))

p.period

p.freq

dev.off()

Error in pdf(paste0(analysis.name, "home/jpincru/pelisdv/pdfs/density/_spectral_density.pdf")): cannot open file 'AFA855_2_R3D_PRJ_trajshome/jpincru/pelisdv/pdfs/density/_spectral_density.pdf'
Traceback:

1. pdf(paste0(analysis.name, "home/jpincru/pelisdv/pdfs/density/_spectral_density.pdf"))