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View Code? Open in Web Editor NEWTronos: TRacking of Nuclear OScillations
License: MIT License
Tronos: TRacking of Nuclear OScillations
License: MIT License
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.
MA_order <- 12
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)
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)
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)
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:
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.
y.spec <- spectrum(y,log="yes",span=2,plot=FALSE,na.action=na.remove)
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:
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