Hi all,
Im trying to make a for loop that makes stacked Density plots per patient.
I made 2 variables Minimum and Maximum in which i determine the minimum and maximum row number of a sample. Which gives me a range.
Doesnt't work (gives me empty plots)
for(i in 1:length(gs)){
png(paste0(Unique_subjects[2],"CD4 CD45 tailgate, ref side left .png") )
plotGate(x = gs[c(Minimum[i]:Maximum[i])], "/stable/nonDebris/Lymphocytes/Singlets/Live/CD3NonDump/CD3+/CD4+/BV786.A+" , xbin = 0 , type = "densityplot", stack = TRUE)
graphics.off()
}
Works partialy (i need an extra graphics.off() often)
png(paste0(Unique_subjects[2],"CD4 CD45 tailgate, ref side left .png") )
plotGate(x = gs[c(Minimum[1]:Maximum[1])], "/stable/nonDebris/Lymphocytes/Singlets/Live/CD3NonDump/CD3+/CD4+/BV786.A+" , xbin = 0 , type = "densityplot", stack = TRUE)
graphics.off()
Works normal:
for(i in 1:length(gs)){
png(filename = paste0("Output/Plots/",gs[[i]]@name,"_.png"),width =40,height = 40,res = 120,units = "cm")
plotGate(gs[[i]],"/stable/nonDebris/Lymphocytes/Singlets/Live/CD3NonDump/CD3+/CD4+/BV786.A+" , default.y="SSC.A",margin=F,smooth=F,merge=T,digits=4,bool=F, type = "densityplot" , showHidden = FALSE,xbins=0, sample.ratio=1,sample.minsize=10000)
graphics.off()
}
The fact that only the stacked density plots gives me this problem, makes me think it has to do specifically with this functionality.
Because sometimes i need to shut the graphical device another time and otherwise i get empty plots. Makes me think the Graphical Devices crashes.
Below i have shown which software versions and packages i am using.
Would anyone have any idea why i am getting empty plots while making stacked density plots?
I am using
R.3.4.4
Rstudio 1.0.153
loaded via a namespace (and not attached):
[1] readxl_1.0.0 changepoint_2.2.2 spam_2.1-4 lazyeval_0.2.1 sp_1.2-7 RPMG_2.2-1
[7] digest_0.6.12 htmltools_0.3.6 rsconnect_0.8.8 magrittr_1.5 memoise_1.1.0 Rwave_2.4-5
[13] ks_1.10.7 matrixStats_0.52.2 R.utils_2.6.0 MCMCpack_1.4-2 colorspace_1.3-2 blob_1.1.1
[19] rrcov_1.4-3 haven_1.1.1 jsonlite_1.5 hexbin_1.27.1 graph_1.54.0 bindr_0.1.1
[25] zoo_1.8-0 glue_1.2.0 gtable_0.2.0 zlibbioc_1.22.0 MatrixModels_0.4-1 car_3.0-0
[31] IDPmisc_1.1.17 Rgraphviz_2.20.0 BiocGenerics_0.22.1 DEoptimR_1.0-8 maps_3.3.0 abind_1.4-5
[37] SparseM_1.77 scales_0.5.0 mvtnorm_1.0-6 multicool_0.1-10 DBI_0.8 Rcpp_0.12.16
[43] xtable_1.8-2 clue_0.3-54 foreign_0.8-69 bit_1.1-12 RSEIS_3.7-4 dotCall64_0.9-04
[49] stats4_3.4.4 htmlwidgets_1.0 FNN_1.1 gplots_3.0.1 RColorBrewer_1.1-2 pkgconfig_2.0.1
[55] XML_3.98-1.10 R.methodsS3_1.7.1 GEOmap_2.4-0 tidyselect_0.2.4 rlang_0.2.0 munsell_0.4.3
[61] cellranger_1.1.0 tools_3.4.4 splancs_2.01-40 stringr_1.2.0 mcmc_0.9-5 knitr_1.20
[67] bit64_0.9-7 robustbase_0.92-8 rgl_0.98.1 caTools_1.17.1 purrr_0.2.4 packrat_0.4.9-1
[73] RBGL_1.52.0 mime_0.5 quantreg_5.35 R.oo_1.21.0 compiler_3.4.4 curl_3.2
[79] tibble_1.4.2 pcaPP_1.9-73 stringi_1.1.7 forcats_0.3.0 fields_9.6 pillar_1.2.1
[85] data.table_1.10.4-3 bitops_1.0-6 corpcor_1.6.9 httpuv_1.3.6.2 R6_2.2.2 latticeExtra_0.6-28
[91] KernSmooth_2.23-15 gridExtra_2.3 RFOC_3.4-3 rio_0.5.10 codetools_0.2-15 MASS_7.3-49
[97] gtools_3.5.0 assertthat_0.2.0 chron_2.3-52 MBA_0.0-9 mnormt_1.5-5 grid_3.4.4
[103] coda_0.19-1 misc3d_0.8-4 carData_3.0-1 Biobase_2.36.2
Hmm, please consider that people are more likely to be able to give a meaningful response if you followed the posting guide and did your homework. In particular,
Thank you for considering.