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pertz-lab
shiny-timecourse-inspector
Commits
d379ec6b
Commit
d379ec6b
authored
Aug 03, 2018
by
dmattek
Browse files
Bug fixes: sparse clustering removed temporarily because sparcl unavailable on CRAN
parent
028696c2
Changes
6
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modules/auxfunc.R
View file @
d379ec6b
...
...
@@ -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
...
...
modules/boxPlot.R
View file @
d379ec6b
...
...
@@ -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
)
...
...
modules/clDistPlot.R
View file @
d379ec6b
...
...
@@ -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
)
...
...
modules/trajRibbonPlot.R
View file @
d379ec6b
...
...
@@ -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
)
...
...
server.R
View file @
d379ec6b
...
...
@@ -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
...
...
ui.R
View file @
d379ec6b
...
...
@@ -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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