A few small updates to the exploratory scripts.

stephenslab · Jul 30, 2024 · 3188e17 · 3188e17
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commit 3188e17
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Showing 2 changed files with 6 additions and 9 deletions.
diff --git a/analysis/examine_newsgroups_more.R b/analysis/examine_newsgroups_more.R
@@ -1,3 +1,4 @@
+# For paper, highlight results with K = 10.
 library(fastTopics)
 library(cowplot)
 set.seed(1)
@@ -10,18 +11,13 @@ n    <- nrow(fit1$L)
 rows <- sample(n,2000)
 fit1 <- select_loadings(fit1,rows)
 fit2 <- select_loadings(fit2,rows)
-tsne <- tsne_from_topics(fit1,dims = 1,verbose = FALSE)
-p1 <- structure_plot(fit1,loadings_order = order(tsne[,1]),topics = 1:k,
-                     grouping = topics[rows])
-p2 <- structure_plot(fit2,loadings_order = order(tsne[,1]),topics = 1:k,
-                     grouping = topics[rows])
+p1 <- structure_plot(fit1,topics = 1:k,grouping = topics[rows])
+p2 <- structure_plot(fit2,topics = 1:k,grouping = topics[rows])
 plot_grid(p1,p2,nrow = 2,ncol = 1)
 
 lda1 <- readRDS("../output/newsgroups/rds/lda-newsgroups-em-k=10.rds")$lda
 lda2 <- readRDS("../output/newsgroups/rds/lda-newsgroups-scd-ex-k=10.rds")$lda
 cor(lda1@gamma,lda2@gamma)
-p3 <- structure_plot(lda1@gamma[rows,],loadings_order = order(tsne[,1]),
-                     topics = 1:k)
-p4 <- structure_plot(lda2@gamma[rows,],loadings_order = order(tsne[,1]),
-                     topics = 1:k)
+p3 <- structure_plot(lda1@gamma[rows,],topics = 1:k)
+p4 <- structure_plot(lda2@gamma[rows,],topics = 1:k)
 plot_grid(p1,p2,p3,p4,nrow = 4,ncol = 1)
diff --git a/analysis/examine_pbmc68k_more.R b/analysis/examine_pbmc68k_more.R
@@ -1,3 +1,4 @@
+# For paper, highlight results with K = 11.
 library(fastTopics)
 library(cowplot)
 set.seed(1)