Commit d379ec6b authored by dmattek's avatar dmattek

Bug fixes: sparse clustering removed temporarily because sparcl unavailable on CRAN

parent 028696c2
......@@ -170,6 +170,26 @@ getClCol <- function(in.dend, in.k) {
#####
## Common plotting functions
myGgplotTheme =
theme_bw(base_size = 8, base_family = "Helvetica") +
theme(
panel.spacing = unit(1, "lines"),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
panel.border = element_blank(),
axis.line.x = element_line(color = "black", size = 0.25),
axis.line.y = element_line(color = "black", size = 0.25),
axis.text = element_text(size = 8),
axis.title = element_text(size = 8),
strip.text = element_text(size = 10, face = "bold"),
strip.background = element_blank(),
legend.key = element_blank(),
legend.text = element_text(size = 8),
legend.key.height = unit(1, "lines"),
legend.key.width = unit(2, "lines"),
legend.position = "top"
)
myGgplotTraj = function(dt.arg, # data table
x.arg, # string with column name for x-axis
y.arg, # string with column name for y-axis
......
......@@ -236,7 +236,8 @@ modBoxPlot = function(input, output, session,
scale_fill_discrete(name = '') +
xlab('') +
ylab('') +
ggplotTheme() +
#ggplotTheme() +
myGgplotTheme +
theme(legend.position = input$selPlotBoxLegendPos)
if (input$chBxAxisLabelsRotate)
......
......@@ -50,6 +50,7 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
ylab("percentage of cells\n") +
xlab("") +
ggplotTheme()
#myGgplotTheme
return(p.out)
......
......@@ -188,6 +188,7 @@ modTrajRibbonPlot = function(input, output, session,
xlab.arg = 'Time (min)',
ylab.arg = '') +
ggplotTheme() +
#myGgplotTheme +
theme(legend.position = input$rBlegendPos)
return(p.out)
......
......@@ -17,7 +17,8 @@ library(d3heatmap) # for interactive heatmap
library(dendextend) # for color_branches
library(colorspace) # for palettes (used to colour dendrogram)
library(RColorBrewer)
library(sparcl) # sparse hierarchical and k-means
# sparcl temporarily unavailable on CRAN
#library(sparcl) # sparse hierarchical and k-means
library(scales) # for percentages on y scale
library(dtw) # for dynamic time warping
library(imputeTS) # for interpolating NAs
......
......@@ -142,12 +142,13 @@ shinyUI(fluidPage(
tabPanel(
'Hierarchical',
clustHierUI('tabClHier')
),
tabPanel(
'Hierarchical Sparse',
clustHierSparUI('tabClHierSpar')
)
# sparse hierarchical clustering package sparcl temporarily unavailable from CRAN
# tabPanel(
# 'Hierarchical Sparse',
# clustHierSparUI('tabClHierSpar')
#)
))
)
))
\ No newline at end of file
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