diff --git a/data-raw/toad-data.R b/data-raw/toad-data.R index 84a5597..28d04d2 100644 --- a/data-raw/toad-data.R +++ b/data-raw/toad-data.R @@ -12,8 +12,8 @@ caneToad.groups <- caneToad.groups[1,] # Build propr object keep <- apply(caneToad.counts, 2, function(x) sum(x >= 10) >= 10) rho <- perb(caneToad.counts, select = keep) -best.99 <- rho[">", .99] -top <- simplify(best.99) +best.995 <- rho[">", .995] +top <- simplify(best.995) # Use data devtools::use_data(caneToad.counts, caneToad.groups, top, overwrite = TRUE) diff --git a/data/top.rda b/data/top.rda index acc5fd4..a7745b7 100644 Binary files a/data/top.rda and b/data/top.rda differ diff --git a/vignettes/visualize.Rmd b/vignettes/visualize.Rmd index cb5c6e1..c9c4bd5 100755 --- a/vignettes/visualize.Rmd +++ b/vignettes/visualize.Rmd @@ -43,10 +43,10 @@ The proportionality metric $\rho$ has two advantages compared to $\phi$. First, rho <- perb(caneToad.counts, select = keep) ``` -Next, we index the most highly proportional pairs based on an arbitrary threshold. In the absence of any statistical testing framework, we set this threshold at $\rho>0.99$ to include only "very proportional" transcript pairs. Alternatively, we could set this threshold at $\rho<-0.99$ to include only "very unproportional" pairs. +Next, we index the most highly proportional pairs based on an arbitrary threshold. In the absence of any statistical testing framework, we set this threshold at $\rho>0.99$ to include only "very proportional" transcript pairs. Alternatively, we could set this threshold at $\rho<-0.99$ to include only "very unproportional" pairs. However, take note that we use a more stringent threshold here so that the vignette renders more quickly. ```{r, eval = FALSE} -best <- rho[">", .99] +best <- rho[">", .995] ``` ## Index-aware Plots @@ -114,7 +114,7 @@ These figures help us conceptualize high-dimensional data and select a highly pr We can extract cluster 3 from the `propr` object using the `subset` method. ```{r, results = "hide"} -sub <- subset(top, select = (clusts == 3)) +sub <- subset(top, select = (clusts == 4)) ``` Now, we can use the `mds` and `snapshot` functions to see how well this cluster differentiates the two experimental groups based on unsupervised methods. We see below in the `mds` plot that projecting our samples across this highly proportional module leads to a near perfect separation between the two experimental groups, excepting the samples "RM0010" and "RM0169". This matches the separation achieved in the source publication which used `edgeR` for feature selection (Rollins 2015).