fix: use R-squared instead of Pearson correlation coefficient (#49)

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: NACHO
 Title: NanoString Quality Control Dashboard
-Version: 2.0.5
+Version: 2.0.6
 Authors@R: 
     c(person(given = "Mickaël",
              family = "Canouil",

NEWS.md

@@ -1,3 +1,10 @@
+# NACHO 2.0.6
+
+## Fixes
+
+- In `R/qc_positive_control.R`,
+  - fix: use R-squared instead of Pearson correlation coefficient. ([#48](https://github.com/mcanouil/NACHO/issues/48))
+
 # NACHO 2.0.5
 
 ## Fixes

R/autoplot.R

@@ -316,14 +316,13 @@ plot_metrics <- function(
         list(
           ggplot2::geom_point(
             data = ~ .x[!(is_outlier)],
-            size = size, width = 0.25, na.rm = TRUE,
+            size = size, na.rm = TRUE,
             position = ggplot2::position_jitter(width = 0.25, height = 0)
           ),
           ggplot2::geom_point(
             data = ~ .x[(is_outlier)],
             size = size * outliers_factor,
             colour = "#b22222",
-            width = 0.25,
             na.rm = TRUE,
             position = ggplot2::position_jitter(width = 0.25, height = 0)
           ),
@@ -338,7 +337,7 @@ plot_metrics <- function(
         )
       } else {
         ggplot2::geom_point(
-          size = size, width = 0.25, na.rm = TRUE,
+          size = size, na.rm = TRUE,
           position = ggplot2::position_jitter(width = 0.25, height = 0)
         )
       }
@@ -449,14 +448,13 @@ plot_cg <- function(
         list(
           ggplot2::geom_point(
             data = ~ .x[!(is_outlier)],
-            size = size, width = 0.25, na.rm = TRUE,
+            size = size, na.rm = TRUE,
             position = ggplot2::position_jitter(width = 0.25, height = 0)
           ),
           ggplot2::geom_point(
             data = ~ .x[(is_outlier)],
             size = size * outliers_factor,
             colour = "#b22222",
-            width = 0.25,
             na.rm = TRUE,
             position = ggplot2::position_jitter(width = 0.25, height = 0)
           ),
@@ -471,7 +469,7 @@ plot_cg <- function(
         )
       } else {
         ggplot2::geom_point(
-          size = size, width = 0.25, na.rm = TRUE,
+          size = size, na.rm = TRUE,
           position = ggplot2::position_jitter(width = 0.25, height = 0)
         )
       }
@@ -1131,7 +1129,7 @@ plot_norm <- function(
     ) +
     ggplot2::geom_line(
       mapping = ggplot2::aes(colour = .data[["Name"]], group = .data[["Name"]]),
-      size = size,
+      linewidth = size,
       na.rm = TRUE
     ) +
     ggplot2::facet_grid(cols = ggplot2::vars(.data[["Status"]])) +

R/qc_positive_control.R

@@ -8,8 +8,12 @@
 #'
 #' @return [[numeric]]
 qc_positive_control <- function(counts) {
-  measured <- log2(counts[["Count"]])
+  if (any(counts[["Count"]] %in% 0)) {
+    measured <- log2(counts[["Count"]] + 1)
+  } else {
+    measured <- log2(counts[["Count"]])
+  }
   known <- log2(as.numeric(sub("^[^(]*\\((.*)\\)$", "\\1", counts[["Name"]]))) # plexset value: "32"
-  correlation <- stats::cor.test(known, measured)$estimate
+  correlation <- summary(stats::lm(measured ~ known))$r.squared
   unname(round(correlation, 5))
 }