mitul-patel
commented
6 years ago Hi Jessica,
Many thanks for trying the tool. Have you installed UMAP and FItSNE before running the app. If not here are the links to install them. UMAP: https://github.com/lmcinnes/umap and FItSNE: https://github.com/KlugerLab/FIt-SNE.
Then you need to specify path for FItSNE (full installation path). Edit scripts/SeuratRUN.R - Change /bin/fasttsne to your path FROM : scObject$val <- RunTSNE(object = scObject$val, reduction.use = "pca", dims.use = 1:75, tsne.method = "FIt-SNE", nthreads = 4, reduction.name = "FItSNE", reduction.key = "FItSNE", fast_tsne_path = "/bin/fast_tsne", max_iter = 2000)
TO: scObject$val <- RunTSNE(object = scObject$val, reduction.use = "pca", dims.use = 1:75, tsne.method = "FIt-SNE", nthreads = 4, reduction.name = "FItSNE", reduction.key = "FItSNE_", fast_tsne_path = "/bin/fast_tsne", max_iter = 2000)
Similarly edit scripts/QCrun.R FROM : scObject$val <- RunTSNE(object = scObject$val, reduction.use = "pca", dims.use = 1:75, tsne.method = "FIt-SNE", nthreads = 4, reduction.name = "FItSNE", reduction.key = "FItSNE_", fast_tsne_path = "/bin/fast_tsne", max_iter = 2000)
TO: scObject$val <- RunTSNE(object = scObject$val, reduction.use = "pca", dims.use = 1:75, tsne.method = "FIt-SNE", nthreads = 4, reduction.name = "FItSNE", reduction.key = "FItSNE_", fast_tsne_path = "/bin/fast_tsne", max_iter = 2000)
I hope it helps. Let me know if you still find any problem.
Regards, Mitul
I loaded the Malignant50.csv file and after selecting the "Quality control and cell filtering" step and clicking Run iS-CellR, I get the following output on R and then it crashes. This is before selecting any quality control/filtering parameters.
Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Warning in normalizePath(path = fast_tsne_path) : path[1]="/bin/fast_tsne": No such file or directory Warning: Error in fftRtsne: fast_tsne_path '/bin/fast_tsne' does not exist or is not executable 81: stop 80: fftRtsne 79: RunTSNE 74: observeEventHandler [/private/var/folders/fv/6p2sdnqx7wl4d2qt_vms4nfm0000gn/T/RtmplS3qff/shinyapp10ffb272e2987/iS-CellR-master/server.R#813] 3: runApp 2: runUrl 1: shiny::runGitHub