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shiny-timecourse-inspector
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pertz-lab
shiny-timecourse-inspector
Commits
f60cefb1
Commit
f60cefb1
authored
Jun 24, 2019
by
Maciej Dobrzynski
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parent
b96c0534
Changes
10
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10 changed files
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22 additions
and
28 deletions
+22
-28
modules-unused/tabClBay.R
modules-unused/tabClBay.R
+0
-0
modules/auxfunc.R
modules/auxfunc.R
+5
-5
modules/dispStats.R
modules/dispStats.R
+8
-3
modules/dispTrackStats.R
modules/dispTrackStats.R
+0
-4
modules/tabAUC.R
modules/tabAUC.R
+0
-2
modules/tabScatter.R
modules/tabScatter.R
+0
-5
modules/trajPlot.R
modules/trajPlot.R
+0
-2
modules/trajPsdPlot.R
modules/trajPsdPlot.R
+0
-3
modules/trajRibbonPlot.R
modules/trajRibbonPlot.R
+0
-1
server.R
server.R
+9
-3
No files found.
modules/tabClBay.R
→
modules
-unused
/tabClBay.R
View file @
f60cefb1
File moved
modules/auxfunc.R
View file @
f60cefb1
...
...
@@ -6,11 +6,11 @@
#
require
(
ggplot2
)
require
(
RColorBrewer
)
require
(
gplots
)
# for heatmap.2
require
(
grid
)
# for modifying grob
require
(
Hmisc
)
# for CI calculation
library
(
ggplot2
)
library
(
RColorBrewer
)
library
(
gplots
)
# for heatmap.2
library
(
grid
)
# for modifying grob
library
(
Hmisc
)
# for CI calculation
# Global parameters ----
...
...
modules/dispStats.R
View file @
f60cefb1
require
(
DT
)
require
(
data.table
)
#
# Time Course Inspector: Shiny app for plotting time series data
# Author: Maciej Dobrzynski
#
# This module is for displaying stats in an interactive table using DT package
#
# UI ----
modStatsUI
=
function
(
id
,
label
=
"Comparing t-points"
)
{
ns
<-
NS
(
id
)
...
...
@@ -11,7 +16,7 @@ modStatsUI = function(id, label = "Comparing t-points") {
)
}
# SERVER ----
modStats
=
function
(
input
,
output
,
session
,
in.data
,
in.meascol
=
'meas.y'
,
...
...
modules/dispTrackStats.R
View file @
f60cefb1
...
...
@@ -5,10 +5,6 @@
# This module is for displaying time series statistics
#
require
(
DT
)
require
(
data.table
)
# UI ----
modTrackStatsUI
=
function
(
id
,
label
=
"Comparing t-points"
)
{
ns
<-
NS
(
id
)
...
...
modules/tabAUC.R
View file @
f60cefb1
...
...
@@ -6,8 +6,6 @@
#
# Calculates area under curve (AUC) for every single time course provided in the input
require
(
pracma
)
# for trapz
# UI ----
modAUCplotUI
=
function
(
id
,
label
=
"Plot Area Under Curves"
)
{
ns
<-
NS
(
id
)
...
...
modules/tabScatter.R
View file @
f60cefb1
...
...
@@ -14,11 +14,6 @@
# callModule(clustHier, 'TabClustHier', dataMod)
# where dataMod is the output from a reactive function that returns dataset ready for clustering
require
(
plotly
)
# interactive plot
require
(
robust
)
require
(
MASS
)
# UI ----
tabScatterPlotUI
<-
function
(
id
,
label
=
"Comparing t-points"
)
{
ns
<-
NS
(
id
)
...
...
modules/trajPlot.R
View file @
f60cefb1
...
...
@@ -6,8 +6,6 @@
#
require
(
DT
)
# UI ----
modTrajPlotUI
=
function
(
id
,
label
=
"Plot Individual Time Series"
)
{
...
...
modules/trajPsdPlot.R
View file @
f60cefb1
...
...
@@ -5,9 +5,6 @@
# This module is for plotting Power Spectral Analysis
#
require
(
DT
)
require
(
scales
)
# UI ----
modPSDPlotUI
=
function
(
id
,
label
=
"Plot PSD of average trajectory."
)
{
ns
<-
NS
(
id
)
...
...
modules/trajRibbonPlot.R
View file @
f60cefb1
...
...
@@ -5,7 +5,6 @@
# This module is for plotting group averages as ribbon plots (mean + 95%CI)
#
require
(
DT
)
modTrajRibbonPlotUI
=
function
(
id
,
label
=
"Plot Individual Time Series"
)
{
ns
<-
NS
(
id
)
...
...
server.R
View file @
f60cefb1
...
...
@@ -10,15 +10,21 @@ library(shinyjs) #http://deanattali.com/shinyjs/
library
(
data.table
)
library
(
ggplot2
)
library
(
gplots
)
# for heatmap.2
library
(
plotly
)
#library(d3heatmap) # for interactive heatmap
library
(
plotly
)
# interactive plot
library
(
DT
)
# interactive tables
library
(
dendextend
)
# for color_branches
library
(
colorspace
)
# for palettes (used to colour dendrogram)
library
(
RColorBrewer
)
library
(
sparcl
)
# sparse hierarchical and k-means
library
(
scales
)
# for percentages on y scale
library
(
sparcl
)
# sparse hierarchical and k-means
library
(
dtw
)
# for dynamic time warping
library
(
imputeTS
)
# for interpolating NAs
library
(
robust
)
# for robust linear regression
library
(
MASS
)
library
(
pracma
)
# for trapz
# Global parameters ----
# change to increase the limit of the upload file size
...
...
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