update visualize.heatmap() to show missing data pattern (fixes #6)

Author: Carol-seven

R/visualizations.R

@@ -95,9 +95,18 @@ visualize.heatmap <- function(dataSet, pkg = "pheatmap",
     plotData <- t(select(dataSet, -c(R.Condition, R.Replicate)))
     colnames(plotData) <- paste0(dataSet$R.Condition, "_", dataSet$R.Replicate)
 
-    pheatmap(mat = plotData,
-             cluster_cols = cluster_cols, cluster_rows = cluster_rows,
-             show_colnames = show_colnames, show_rownames = show_rownames)
+    if (anyNA(plotData)) {
+      plotData <- ifelse(is.na(plotData), 0, 1)
+      pheatmap(mat = plotData,
+               color = c("white", "black"), legend_breaks = c(0, 1),
+               legend_labels = c("Missing value", "Valid value"),
+               cluster_cols = cluster_cols, cluster_rows = cluster_rows,
+               show_colnames = show_colnames, show_rownames = show_rownames)
+    } else {
+      pheatmap(mat = plotData,
+               cluster_cols = cluster_cols, cluster_rows = cluster_rows,
+               show_colnames = show_colnames, show_rownames = show_rownames)
+    }
 
   } else if (pkg == "ggplot2") {
 
@@ -107,15 +116,27 @@ visualize.heatmap <- function(dataSet, pkg = "pheatmap",
       select(-c(R.Condition, R.Replicate)) %>%
       pivot_longer(-R.ConRep)
 
-    ggplot(plotData, aes(x = R.ConRep, y = name, fill = value)) +
-      geom_tile() +
-      guides(fill = guide_colourbar(title = NULL)) +
-      scale_y_discrete(limits = rev) +
-      scale_fill_distiller(palette = "RdYlBu") +
-      theme(axis.text.x = element_text(angle = -90, vjust = .5)) +
-      xlab(NULL) +
-      ylab(NULL)
-    
+    if (anyNA(plotData$value)) {
+      ggplot(plotData, aes(x = R.ConRep, y = name, fill = factor(!is.na(value)))) +
+        geom_tile(color = "grey60") +
+        guides(fill = guide_legend(title = NULL)) +
+        scale_fill_manual(values = c("TRUE" = "black", "FALSE" = "white"),
+                          labels = c("FALSE" = "Missing value", "TRUE" = "Valid value"),
+                          drop = FALSE) +
+        scale_y_discrete(limits = rev) +
+        theme(axis.text.x = element_text(angle = -90, vjust = .5)) +
+        xlab(NULL) +
+        ylab(NULL)
+    } else {
+      ggplot(plotData, aes(x = R.ConRep, y = name, fill = value)) +
+        geom_tile(color = "grey60") +
+        guides(fill = guide_colourbar(title = NULL)) +
+        scale_y_discrete(limits = rev) +
+        scale_fill_distiller(palette = "RdYlBu") +
+        theme(axis.text.x = element_text(angle = -90, vjust = .5)) +
+        xlab(NULL) +
+        ylab(NULL)
+    }
   }
 }
 

docs/articles/visualization.html

@@ -75,6 +75,18 @@ visualize.heatmap(dataImput, pkg = "pheatmap",
 When protein names are excessively long, it is recommended to set
 `show_rownames = FALSE` to view the full heatmap.
 
+If the input data contains an NA value, the heatmap will be binary for
+missing data patterns, i.e., whether values are present or absent.
+
+``` r
+
+visualize.heatmap(dataSet, pkg = "pheatmap",
+                  cluster_cols = TRUE, cluster_rows = TRUE,
+                  show_colnames = TRUE, show_rownames = TRUE)
+```
+
+![](visualization_files/figure-html/unnamed-chunk-5-1.png)
+
 - Option 2 use the source package `ggplot2` to generate a ggplot object
   but does not include the dendrogram.
 
@@ -83,12 +95,19 @@ When protein names are excessively long, it is recommended to set
 visualize.heatmap(dataImput, pkg = "ggplot2")
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-5-1.png)
+![](visualization_files/figure-html/unnamed-chunk-6-1.png)
 
 In a heatmap, similar colors within a row indicate relatively consistent
 values, suggesting similar protein expression levels across different
 samples.
 
+``` r
+
+visualize.heatmap(dataSet, pkg = "ggplot2")
+```
+
+![](visualization_files/figure-html/unnamed-chunk-7-1.png)
+
 ## MA plot
 
 ### Examples
@@ -100,7 +119,7 @@ visualize.ma(anlys_ma$`100pmol-50pmol`, M.thres = 1)
 #> (`geom_text_repel()`).
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-6-1.png)
+![](visualization_files/figure-html/unnamed-chunk-8-1.png)
 
 where `M.thres = 1` means the M thresholds are set to -1 and 1. The
 scatters are split into three parts: up regulation (M \> 1), no
@@ -118,7 +137,7 @@ visualize.ma(anlys_ma, M.thres = 1)
 #> (`geom_text_repel()`).
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-7-1.png)
+![](visualization_files/figure-html/unnamed-chunk-9-1.png)
 
 ### Details
 
@@ -165,7 +184,7 @@ visualize.rank(dataImput, listName = "POLK_HUMAN",
                facet = c("Replicate", "Condition"))
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-8-1.png)
+![](visualization_files/figure-html/unnamed-chunk-10-1.png)
 
 ## Histogram of fold changes and p-values for test
 
@@ -176,7 +195,7 @@ visualize.rank(dataImput, listName = "POLK_HUMAN",
 visualize.test(anlys_modt$`100pmol-50pmol`)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-9-1.png)
+![](visualization_files/figure-html/unnamed-chunk-11-1.png)
 
 If the input `dataSet` is the whole list `anlys_modt`, **msDiaLogue**
 will produce individual subplots corresponding to each comparison.
@@ -186,7 +205,7 @@ will produce individual subplots corresponding to each comparison.
 visualize.test(anlys_modt)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-10-1.png)
+![](visualization_files/figure-html/unnamed-chunk-12-1.png)
 
 ### Details
 
@@ -211,7 +230,7 @@ combinations of sets.
 visualize.upset(dataSet)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-11-1.png)
+![](visualization_files/figure-html/unnamed-chunk-13-1.png)
 
 This plot reveals that 42 proteins are shared by 50pmol, 100pmol, and
 200pmol, while only 3 proteins are shared by 100 pmol and 200pmol, but
@@ -230,7 +249,7 @@ visualize.venn(dataSet, show_percentage = TRUE,
                saveRes = TRUE)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-12-1.png)
+![](visualization_files/figure-html/unnamed-chunk-14-1.png)
 
 where `saveRes = TRUE` refers to the data containing logical columns
 representing sets in Venn plot information will be saved as a .csv file
@@ -251,7 +270,7 @@ visualize.volcano(anlys_modt$`100pmol-50pmol`, P.thres = 0.05, F.thres = 1)
 #> (`geom_text_repel()`).
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-13-1.png)
+![](visualization_files/figure-html/unnamed-chunk-15-1.png)
 
 If the input `dataSet` is the whole list `anlys_modt`, **msDiaLogue**
 will produce individual subplots corresponding to each comparison.
@@ -263,7 +282,7 @@ visualize.volcano(anlys_modt, P.thres = 0.05, F.thres = 1)
 #> (`geom_text_repel()`).
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-14-1.png)
+![](visualization_files/figure-html/unnamed-chunk-16-1.png)
 
 ### Details
 
@@ -291,7 +310,7 @@ visualize.scree(anlys_pca, type = c("bar", "line"),
                 label = TRUE, ncp = 10)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-15-1.png)
+![](visualization_files/figure-html/unnamed-chunk-17-1.png)
 
 where `label = TRUE` adds information labels at the top of bars/points,
 and `ncp = 10` sets the number of dimension to be displayed.
@@ -305,7 +324,7 @@ and `ncp = 10` sets the number of dimension to be displayed.
 visualize.score(anlys_pca, ellipse = TRUE, ellipse.level = 0.95, label = TRUE)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-16-1.png)
+![](visualization_files/figure-html/unnamed-chunk-18-1.png)
 
 ### Details
 
@@ -329,7 +348,7 @@ provided), for each groups (condition) provided.
 visualize.loading(anlys_pca, label = TRUE)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-17-1.png)
+![](visualization_files/figure-html/unnamed-chunk-19-1.png)
 
 ### Details
 
@@ -353,7 +372,7 @@ number of proteins, this plot can be unwieldy.
 visualize.biplot(anlys_pca, ellipse = TRUE, ellipse.level = 0.95, label = "all")
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-18-1.png)
+![](visualization_files/figure-html/unnamed-chunk-20-1.png)
 
 ## VIP score plot
 
@@ -370,7 +389,7 @@ each condition.
 visualize.vip(anlys_plsda, comp = 1, num = 10, thres = 1)
 ```
 
-![](visualization_files/figure-html/unnamed-chunk-19-1.png)
+![](visualization_files/figure-html/unnamed-chunk-21-1.png)
 
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