clean up

Author: taiyun

.gitignore

@@ -1,6 +1,7 @@
 .Rproj.user
 .Rhistory
 .RData
+.lintr
 vignettes/webimg/
 inst/doc/
 #!vignettes/webimg/rectangles-1.png

R/colorlegend.R

@@ -34,6 +34,7 @@ colorlegend = function(
   addlabels = TRUE,
   ...)
 {
+
   if (is.null(at) && addlabels) {
     at = seq(0L, 1L, length = length(labels))
   }
@@ -106,7 +107,7 @@ colorlegend = function(
       }
 
       if(align == 'c') {
-        text(x = at, y = ylim[1],    labels = labels, pos = 2, ...)
+        text(x = at, y = ylim[1], labels = labels, pos = 2, ...)
       }
 
       if(align == 'r') {

R/colors.R

@@ -31,8 +31,8 @@ COL2 = function(diverging = c('RdBu', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdYlBu'),
              '#D9F0D3', '#A6DBA0', '#5AAE61', '#1B7837', '#00441B'),
     PuOr = c('#7F3B08', '#B35806', '#E08214', '#FDB863', '#FEE0B6', '#FFFFFF',
              '#D8DAEB', '#B2ABD2', '#8073AC', '#542788', '#2D004B'),
-    RdYlBu = c('#a50026','#d73027','#f46d43','#fdae61','#fee090','#FFFFFF',
-                '#e0f3f8','#abd9e9','#74add1','#4575b4','#313695')
+    RdYlBu = c('#A50026', '#D73027', '#F46D43', '#FDAE61', '#FEE090', '#FFFFFF',
+               '#E0F3F8', '#ABD9E9', '#74ADD1', '#4575B4', '#313695')
   )
 
   return(colorRampPalette(colors)(n))

R/cor-mtest.R

@@ -27,13 +27,13 @@ cor.mtest = function(mat, ...) {
   for (i in 1:(n - 1)) {
     for (j in (i + 1):n) {
 
-      tmp = cor.test(x = mat[,i], y = mat[,j], ...)
-      p.mat[i,j] = p.mat[j,i] = tmp$p.value
+      tmp = cor.test(x = mat[, i], y = mat[, j], ...)
+      p.mat[i, j] = p.mat[j, i] = tmp$p.value
 
       # only 'pearson' method provides confidence intervals
       if (!is.null(tmp$conf.int)) {
-        lowCI.mat[i,j] = lowCI.mat[j,i] = tmp$conf.int[1]
-        uppCI.mat[i,j] = uppCI.mat[j,i] = tmp$conf.int[2]
+        lowCI.mat[i, j] = lowCI.mat[j, i] = tmp$conf.int[1]
+        uppCI.mat[i, j] = uppCI.mat[j, i] = tmp$conf.int[2]
       }
     }
   }

R/corrMatOrder.R

@@ -37,8 +37,9 @@ corrMatOrder = function(
   corr,
   order = c('AOE', 'FPC', 'hclust', 'alphabet'),
   hclust.method = c('complete', 'ward', 'ward.D', 'ward.D2', 'single',
-                    'average', 'mcquitty', 'median', 'centroid') )
+                    'average', 'mcquitty', 'median', 'centroid'))
 {
+
   order = match.arg(order)
   hclust.method = match.arg(hclust.method)
 

R/corrRect.R

@@ -31,7 +31,8 @@
 #' @author Taiyun Wei
 #' @export
 corrRect = function(corrRes = NULL, index = NULL, name = NULL, namesMat = NULL,
-                    col = 'black', lwd = 2, ...) {
+                    col = 'black', lwd = 2, ...)
+{
 
   if((as.integer(!is.null(index)) + as.integer(!is.null(name)) +
       as.integer(!is.null(namesMat))) > 1) {
@@ -81,20 +82,20 @@ corrRect = function(corrRes = NULL, index = NULL, name = NULL, namesMat = NULL,
     y2 = nrow(corr) - index[-1] + 0.5
     St = S = cbind(c(x1, x1, x2, x2), c(y1, y1, y2, y2),
                    c(x2, x1, x2, x1), c(y1, y2, y1, y2))
-    St[,2] = abs(St[,2] - nrow(corr) - 1)
-    St[,4] = abs(St[,4] - nrow(corr) - 1)
+    St[, 2] = abs(St[, 2] - nrow(corr) - 1)
+    St[, 4] = abs(St[, 4] - nrow(corr) - 1)
 
     if(type=='upper') {
-      i = which((St[,1] - St[,2]) > -0.1 & (St[,3] - St[,4]) > -0.1)
-      S = S[i,]
+      i = which((St[, 1] - St[, 2]) > -0.1 & (St[, 3] - St[, 4]) > -0.1)
+      S = S[i, ]
     }
 
     if(type=='lower') {
-      i = which((St[,2] - St[,1]) > -0.1 & (St[,4] - St[,3]) > -0.1)
-      S = S[i,]
+      i = which((St[, 2] - St[, 1]) > -0.1 & (St[, 4] - St[, 3]) > -0.1)
+      S = S[i, ]
     }
 
-    segments(S[,1], S[,2], S[,3], S[,4], col=col, lwd = lwd, ...)
+    segments(S[, 1], S[, 2], S[, 3], S[, 4], col = col, lwd = lwd, ...)
   }
 
   if(!is.null(namesMat)) {
@@ -108,10 +109,10 @@ corrRect = function(corrRes = NULL, index = NULL, name = NULL, namesMat = NULL,
 
     xy = cbind(xy1, xy2)
 
-    x1 = apply(xy[, c(1,3), drop=FALSE], 1, min) - 0.5
-    y1 = apply(xy[, c(2,4), drop=FALSE], 1, min) - 0.5
-    x2 = apply(xy[, c(1,3), drop=FALSE], 1, max) + 0.5
-    y2 = apply(xy[, c(2,4), drop=FALSE], 1, max) + 0.5
+    x1 = apply(xy[, c(1, 3), drop=FALSE], 1, min) - 0.5
+    y1 = apply(xy[, c(2, 4), drop=FALSE], 1, min) - 0.5
+    x2 = apply(xy[, c(1, 3), drop=FALSE], 1, max) + 0.5
+    y2 = apply(xy[, c(2, 4), drop=FALSE], 1, max) + 0.5
 
     rect(x1, y1, x2, y2, border = col, lwd = lwd, ...)
   }
@@ -123,13 +124,13 @@ corrRect = function(corrRes = NULL, index = NULL, name = NULL, namesMat = NULL,
 
 #' @note pure function
 #' @noRd
-getCharXY = function(x, dat){
+getCharXY = function(x, dat) {
 
-  res = apply(x, 1, function(n, d=dat) d[d[,1]==n[1]&d[,2]==n[2], 3:4])
+  res = apply(x, 1, function(n, d=dat) d[d[, 1]==n[1]&d[, 2]==n[2], 3:4])
 
   f = which(unlist(lapply(res, nrow))==0)
   if(length(f) > 0) {
-    error  = paste(toString(unique(x[f,])), 'paired X-Y names were not found!')
+    error  = paste(toString(unique(x[f, ])), 'paired X-Y names were not found!')
     stop(error)
   }
 

R/corrRect.hclust.R

@@ -28,8 +28,9 @@ corrRect.hclust = function(
   col = 'black',
   lwd = 2,
   method = c('complete', 'ward', 'ward.D', 'ward.D2', 'single', 'average',
-             'mcquitty', 'median', 'centroid') )
+             'mcquitty', 'median', 'centroid'))
 {
+
   n = nrow(corr)
   method = match.arg(method)
   tree = hclust(as.dist(1 - corr), method = method)