support with own data for visualization

Author: junjunlab

.Rhistory

@@ -413,3 +413,7 @@ library(devtools)
 document()
 check()
 install()
+library(devtools)
+document()
+check()
+install()

R/visCluster.R

@@ -3,6 +3,7 @@
 #' @title using visCluster to visualize cluster results from clusterData output
 #'
 #' @param object clusterData object, default NULL.
+#' @param plot.data supply with own data with data.frame format for visualization, default NULL.
 #' @param ht.col heatmap colors, default c("blue", "white", "red").
 #' @param border whether add border for heatmap, default TRUE.
 #' @param plot.type the plot type to choose which incuding "line","heatmap" and "both".
@@ -77,6 +78,7 @@ globalVariables(c('cell_type', 'cluster.num', 'gene',"ratio","bary",
                   'membership', 'norm_value','id', 'log10P', 'pval',
                   'Var1'))
 visCluster <- function(object = NULL,
+                       plot.data = NULL,
                        ht.col = c("blue", "white", "red"),
                        border = TRUE,
                        plot.type = c("line","heatmap","both"),
@@ -133,7 +135,11 @@ visCluster <- function(object = NULL,
   # choose plot type
   if(plot.type == "line"){
     # process data
-    data <- data.frame(object$long.res)
+    if(is.null(plot.data)){
+      data <- data.frame(object$long.res)
+    }else{
+      data <- plot.data
+    }
 
     # sample orders
     if(!is.null(sample.order)){
@@ -193,7 +199,11 @@ visCluster <- function(object = NULL,
   }else{
     # ==========================================================================
     # process data
-    data <- data.frame(object$wide.res)
+    if(is.null(plot.data)){
+      data <- data.frame(object$wide.res)
+    }else{
+      data <- plot.data
+    }
 
     # prepare matrix
     if(object$type == "mfuzz"){