analyze: fix the factor level consistent with the input

uconn-scs · Mar 11, 2024 · f6d551f · f6d551f
1 parent 04a222a
commit f6d551f
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Showing 17 changed files with 17 additions and 17 deletions.
diff --git a/R/analyze.R b/R/analyze.R
@@ -103,7 +103,7 @@ analyze <- function(dataSet, conditions, testType = "t-test") {
   } else if (testType == "mod.t-test") {
 
     ## construct the design matrix
-    conditions <- factor(filteredData$R.Condition, labels = LETTERS[1:2])
+    conditions <- factor(filteredData$R.Condition, levels = conditions, labels = LETTERS[1:2])
     design <- model.matrix(~ 0 + conditions)
 
     ## fit linear model for each protein

diff --git a/docs/articles/usage_template.html b/docs/articles/usage_template.html
diff --git a/docs/articles/usage_template_files/figure-html/unnamed-chunk-41-1.png b/docs/articles/usage_template_files/figure-html/unnamed-chunk-41-1.png
diff --git a/docs/articles/usage_template_files/figure-html/unnamed-chunk-44-1.png b/docs/articles/usage_template_files/figure-html/unnamed-chunk-44-1.png
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   usage_template: usage_template.html
-last_built: 2024-03-07T23:23Z
+last_built: 2024-03-11T20:22Z
 urls:
   reference: https://uconn-scs.github.io/msDiaLogue/reference
   article: https://uconn-scs.github.io/msDiaLogue/articles

diff --git a/tests/visualization/MA.pdf b/tests/visualization/MA.pdf
diff --git a/tests/visualization/PCA_biplot.pdf b/tests/visualization/PCA_biplot.pdf
diff --git a/tests/visualization/PCA_ind.pdf b/tests/visualization/PCA_ind.pdf
diff --git a/tests/visualization/PCA_scree.pdf b/tests/visualization/PCA_scree.pdf
diff --git a/tests/visualization/PCA_var.pdf b/tests/visualization/PCA_var.pdf
diff --git a/tests/visualization/Upset.pdf b/tests/visualization/Upset.pdf
diff --git a/tests/visualization/Venn.pdf b/tests/visualization/Venn.pdf
diff --git a/tests/visualization/heatmap_ggplot2.pdf b/tests/visualization/heatmap_ggplot2.pdf
diff --git a/tests/visualization/heatmap_pheatmap.pdf b/tests/visualization/heatmap_pheatmap.pdf
diff --git a/tests/visualization/normalize.pdf b/tests/visualization/normalize.pdf
diff --git a/tests/visualization/t-test.pdf b/tests/visualization/t-test.pdf
diff --git a/tests/visualization/volcano.pdf b/tests/visualization/volcano.pdf