spatPlot2D not recognizing color vector fi select: point shape="voronoi" about giotto HOT 5 CLOSED

On Tue, Oct 19, 2021 at 7:58 PM Ruben Dries ***@***.***> wrote: Hi Stefano, I have been trying to reproduce this bug, but it actually works fine on my end. Here is a small example you can run in less than a minute. It did use the development version, which has a couple of other bug fixes but is otherwise completely the same as the current version. ***@***.***") library(Giotto) temp_dir = '~/Temp/' myinstructions = createGiottoInstructions(save_dir = temp_dir, save_plot = FALSE, return_plot = TRUE, show_plot = FALSE) expr_path = system.file("extdata", "seqfish_field_expr.txt.gz", package = 'Giotto') loc_path = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto') seqfish_mini <- createGiottoObject(raw_exprs = expr_path, spatial_locs = loc_path, instructions = myinstructions) # processing seqfish_mini <- filterGiotto(gobject = seqfish_mini, expression_threshold = 0.5, gene_det_in_min_cells = 20, min_det_genes_per_cell = 0) seqfish_mini <- normalizeGiotto(gobject = seqfish_mini, scalefactor = 6000, verbose = T) seqfish_mini <- addStatistics(gobject = seqfish_mini) seqfish_mini <- adjustGiottoMatrix(gobject = seqfish_mini, expression_values = c('normalized'), covariate_columns = c('nr_genes', 'total_expr')) # dimension reduction seqfish_mini <- calculateHVG(gobject = seqfish_mini) seqfish_mini <- runPCA(gobject = seqfish_mini) seqfish_mini <- runUMAP(seqfish_mini, dimensions_to_use = 1:5, n_threads = 2) seqfish_mini <- createNearestNetwork(gobject = seqfish_mini, dimensions_to_use = 1:5, k = 5) seqfish_mini <- doLeidenCluster(gobject = seqfish_mini, resolution = 0.4, n_iterations = 1000) ## provide annotation for the leiden identified groups clusters_cell_types = c('cell A', 'cell B', 'cell C', 'cell D', 'cell E', 'cell F', 'cell G', 'cell H') names(clusters_cell_types) = 1:8 seqfish_mini = annotateGiotto(gobject = seqfish_mini, annotation_vector = clusters_cell_types, cluster_column = 'leiden_clus', name = 'cell_types') ## default colors spatPlot2D(gobject = seqfish_mini, point_shape = 'border', cell_color = 'cell_types') spatPlot2D(gobject = seqfish_mini, point_shape = 'no_border', cell_color = 'cell_types') spatPlot2D(gobject = seqfish_mini, point_shape = 'voronoi', cell_color = 'cell_types') ## identify your own colors my_color_code = c('blue', 'pink', 'green', 'yellow', 'purple', 'black', 'orange', 'brown') names(my_color_code) = clusters_cell_types spatPlot2D(gobject = seqfish_mini, point_shape = 'border', cell_color = 'cell_types', cell_color_code = my_color_code, point_size = 3) spatPlot2D(gobject = seqfish_mini, point_shape = 'no_border', cell_color = 'cell_types', cell_color_code = my_color_code, point_size = 3) spatPlot2D(gobject = seqfish_mini, point_shape = 'voronoi', cell_color = 'cell_types', cell_color_code = my_color_code) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/RubD/Giotto/issues/141#issuecomment-947193313>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEBOCZSLTF2QAHZSRSWYV7DUHYA3XANCNFSM5F4GHQ4Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

Hello Ruben, Thanks a lot for looking into this. Indeed, it looks very strange. I guess I am doing something wrong and I am not realizing it. Anyway I have installed the new version and I will try to do a voronoi plot following your suggestion. I have actually one question that I think is also relevant for all the Giotto users: is the Giotto object I have created with Giotto compatible with the new version , Giotto Suite? I really appreciated your help. Thanks in advance. Kind Regards, *Stefano Nardone, PhD * research scientist, Harvard Medical School Beth Israel Deaconess Medical Center Center for Life Sciences, 3 Blackfan Circle, Boston, MA 02115 phone +1 413-695-1678 On Tue, Oct 19, 2021 at 7:58 PM Ruben Dries ***@***.***> wrote: > Hi Stefano, > > I have been trying to reproduce this bug, but it actually works fine on > my end. > > Here is a small example you can run in less than a minute. It did use the > development version, which has a couple of other bug fixes but is otherwise > completely the same as the current version. > > ***@***.***") > > library(Giotto) > > temp_dir = '~/Temp/' > myinstructions = createGiottoInstructions(save_dir = temp_dir, > save_plot = FALSE, > return_plot = TRUE, > show_plot = FALSE) > > expr_path = system.file("extdata", "seqfish_field_expr.txt.gz", package = 'Giotto') > loc_path = system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto') > seqfish_mini <- createGiottoObject(raw_exprs = expr_path, > spatial_locs = loc_path, > instructions = myinstructions) > > # processing > seqfish_mini <- filterGiotto(gobject = seqfish_mini, > expression_threshold = 0.5, > gene_det_in_min_cells = 20, > min_det_genes_per_cell = 0) > seqfish_mini <- normalizeGiotto(gobject = seqfish_mini, scalefactor = 6000, verbose = T) > seqfish_mini <- addStatistics(gobject = seqfish_mini) > seqfish_mini <- adjustGiottoMatrix(gobject = seqfish_mini, > expression_values = c('normalized'), > covariate_columns = c('nr_genes', 'total_expr')) > > # dimension reduction > seqfish_mini <- calculateHVG(gobject = seqfish_mini) > seqfish_mini <- runPCA(gobject = seqfish_mini) > seqfish_mini <- runUMAP(seqfish_mini, dimensions_to_use = 1:5, n_threads = 2) > seqfish_mini <- createNearestNetwork(gobject = seqfish_mini, dimensions_to_use = 1:5, k = 5) > seqfish_mini <- doLeidenCluster(gobject = seqfish_mini, resolution = 0.4, n_iterations = 1000) > > > ## provide annotation for the leiden identified groups > clusters_cell_types = c('cell A', 'cell B', 'cell C', 'cell D', > 'cell E', 'cell F', 'cell G', 'cell H') > names(clusters_cell_types) = 1:8 > seqfish_mini = annotateGiotto(gobject = seqfish_mini, > annotation_vector = clusters_cell_types, > cluster_column = 'leiden_clus', > name = 'cell_types') > > ## default colors > spatPlot2D(gobject = seqfish_mini, point_shape = 'border', cell_color = 'cell_types') > spatPlot2D(gobject = seqfish_mini, point_shape = 'no_border', cell_color = 'cell_types') > spatPlot2D(gobject = seqfish_mini, point_shape = 'voronoi', cell_color = 'cell_types') > > ## identify your own colors > my_color_code = c('blue', 'pink', 'green', 'yellow', > 'purple', 'black', 'orange', 'brown') > names(my_color_code) = clusters_cell_types > > spatPlot2D(gobject = seqfish_mini, point_shape = 'border', cell_color = 'cell_types', cell_color_code = my_color_code, point_size = 3) > spatPlot2D(gobject = seqfish_mini, point_shape = 'no_border', cell_color = 'cell_types', cell_color_code = my_color_code, point_size = 3) > spatPlot2D(gobject = seqfish_mini, point_shape = 'voronoi', cell_color = 'cell_types', cell_color_code = my_color_code) > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <https://github.com/RubD/Giotto/issues/141#issuecomment-947193313>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AEBOCZSLTF2QAHZSRSWYV7DUHYA3XANCNFSM5F4GHQ4Q> > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> > or Android > <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > >