Added volcano plots to annotate_newsgroups analysis.

Author: pcarbo

analysis/annotate_newsgroups.Rmd

@@ -149,3 +149,25 @@ ggsave("structure_plot_newsgroups_topics.png",p1,
 ggsave("structure_plot_other_topics.png",p2,
        height = 2,width = 8,dpi = 200,bg = "white")
 ```
+
+### Annotation of the factors using "distinctive words"
+
+ADD TEXT HERE.
+
+```{r volcano-plot-k1, fig.height=3.5, fig.width=4.5}
+volcano_plot(de_le,k = "k1",ymax = 30)
+```
+
+ADD MORE TEXT HERE.
+
+```{r more-volcano-plots, fig.height=9, fig.width=7}
+plot_grid(volcano_plot(de_le,k = "k3") + guides(color = "none"),
+          volcano_plot(de_le,k = "k6") + guides(color = "none"),
+          volcano_plot(de_le,k = "k7",ymax = 30) + guides(color = "none"),
+          volcano_plot(de_le,k = "k8",ymax = 60) + guides(color = "none"),
+          volcano_plot(de_le,k = "k9",ymax = 40)  + guides(color = "none"),
+		  volcano_plot(de_le,k = "k10",ymax = 40) + guides(color = "none"),
+		  nrow = 3,ncol = 2)
+```
+
+TO DO NEXT: Generate "distinctive feature" scatterplots.

analysis/newsgroups_annotate.R

@@ -1,18 +1,6 @@
 #
 # TO DO NEXT:
-# - Move this code to newsgroups_annotate.Rmd.
 # - Generate the "effects matrices" (F_le, F_vsnull), that we will analyze.
 # - Create "distinctive features" scatterplots.
 # - Design the "effects plot" on paper first (no R code).
 #
-
-# Volcano plots using "least extreme" LFCs.
-p1 <- volcano_plot(de_le,k = "k1",ymax = 30)
-p2 <- volcano_plot(de_le,k = "k2",ymax = 100)
-p3 <- volcano_plot(de_le,k = "k3")
-p5 <- volcano_plot(de_le,k = "k5",ymax = 80)
-p6 <- volcano_plot(de_le,k = "k6")
-p7 <- volcano_plot(de_le,k = "k7",ymax = 30)
-p8 <- volcano_plot(de_le,k = "k8",ymax = 60)
-p9 <- volcano_plot(de_le,k = "k9",ymax = 40)
-p10 <- volcano_plot(de_le,k = "k10",ymax = 40)