Change text for outliers in the last part of the PCA report

umr1283 · Jun 10, 2020 · 9efff58 · 9efff58
1 parent b854aea
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rain
 Title: Reference-based Ancestry INference
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: 
     c(person(given = "Mickaël",
              family = "Canouil",

diff --git a/NEWS.md b/NEWS.md
@@ -1,17 +1,26 @@
+# rain 0.4.1
+
+## Minor text improvements
+
+* In `R/pca_report.R`,
+    + Change text for outliers in the last part of the PCA report.
+
 # rain 0.4.0
 
+## Minor improvements and fixes
+
 * In `DESCRIPTION`,
-  + Use `patchwork` for ethnicity plot.
-  + Remove `gcta64` from system requirements.
+    + Use `patchwork` for ethnicity plot.
+    + Remove `gcta64` from system requirements.
 * In `R/compute_pca.R`,
-  + Use `R.utils` to count number of SNPs from `*.bim` file.
-  + Fix number of SNPs in ggplot legend.
-  + Fix a missplaced `.data` pronoun.
-  + Core code rewrite.
-  + Change messages prefix.
-* In `/R/pca_report.R`, 
-  + Add packages prefix for `tidyselect`.
-  + Update to `ggplot2` `v3.3.0`.
+    + Use `R.utils` to count number of SNPs from `*.bim` file.
+    + Fix number of SNPs in ggplot legend.
+    + Fix a missplaced `.data` pronoun.
+    + Core code rewrite.
+    + Change messages prefix.
+* In `R/pca_report.R`, 
+    + Add packages prefix for `tidyselect`.
+    + Update to `ggplot2` `v3.3.0`.
 
 # rain 0.3.0
 

diff --git a/R/pca_report.R b/R/pca_report.R
@@ -187,10 +187,10 @@ pca_report <- function(
         dist_centre = NULL,
         high = NULL,
         low = NULL,
-        bad_samples = factor(ifelse(.data[["bad_samples_bool"]], "BAD", "GOOD"), levels = c("BAD", "GOOD"))
+        is_outliers = factor(ifelse(.data[["bad_samples_bool"]], "Yes", "No"), levels = c("Yes", "No"))
       )
 
-    ivar <- "bad_samples"
+    ivar <- "is_outliers"
     p <- paste0("PC", 1:fig_n_comp) %>%
       utils::combn(2) %>%
       t() %>%
@@ -212,7 +212,7 @@ pca_report <- function(
       ggplot2::geom_point(shape = 4, size = 2, na.rm = TRUE) +
       ggplot2::stat_ellipse(type = "norm", na.rm = TRUE) +
       ggplot2::scale_colour_viridis_d() +
-      ggplot2::labs(x = NULL, y = NULL) +
+      ggplot2::labs(x = NULL, y = NULL, colour = "Outliers") +
       ggplot2::facet_grid(
         rows = ggplot2::vars(!!ggplot2::sym("Y.PC")),
         cols = ggplot2::vars(!!ggplot2::sym("X.PC")),