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STT200 Shiny Apps
Intro Statistics Applets
Commits
1d263249
Commit
1d263249
authored
5 years ago
by
Manski, Scott
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TwoProportionResamplingTest/TwoProportionResamplingTest.R
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TwoProportionResamplingTest/TwoProportionResamplingTest.R
TwoProportionResamplingTest/TwoProportionSource.R
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1d263249
# ------------------------------------------------------------------------------
# File: TwoProportionResamplingTest.R
# Authors: Camille Fairbourn, Scott Manski
# Date: 03/26/2019
# Desc: This app performs a two proportion test via randomization. The
# resampling test mimics Fisher's Exact Test.
# Published Location:
# Email: fairbour@msu.edu, manskisc@msu.edu
#
# For questions or concerns, please email the authors. This work is licensed
# under a Creative Commons Attribution-ShareAlike 4.0 International License
# (https://creativecommons.org/licenses/by-sa/4.0/).
# ------------------------------------------------------------------------------
# loading packages
library
(
shiny
)
library
(
ggplot2
)
library
(
dplyr
)
library
(
BHH2
)
library
(
gridExtra
)
library
(
shinyjs
)
enableBookmarking
(
store
=
"server"
)
# Sources objects, functions, etc, from TwoProportionSource.R
# This file contains the html code for the editable table,
# the decimalcount function, the dotplot_locs function, and
# custom ggplot2 themes.
source
(
"TwoProportionSource.R"
)
# defines the presets
Presets
<-
list
()
# Presets`preset name` <- c(Top Left, Bottom Left, Top Right, Bottom Right,
# Column A Name, Column B name, Row A name, Row B name)
Presets
$
`Duct Tape Therapy`
<-
c
(
22
,
15
,
4
,
10
,
"Wart Gone"
,
"Wart Remains"
,
"Duct Tape"
,
"Cryotherapy"
)
Presets
$
`Gender Discrimination`
<-
c
(
21
,
14
,
3
,
10
,
"Promotion"
,
"No Promotion"
,
"Male"
,
"Female"
)
Presets
$
`Opportunity Cost`
<-
c
(
56
,
41
,
19
,
34
,
"buy DVD"
,
"not buy DVD"
,
"control"
,
"treatment"
)
Presets
$
`Avandia`
<-
c
(
2593
,
5386
,
65000
,
154592
,
"Yes"
,
"No"
,
"Rosiglitazone"
,
"Pioglitazone"
)
Presets
$
`Custom`
<-
c
(
0
,
0
,
0
,
0
,
"Column A"
,
"Column B"
,
"Row 1"
,
"Row 2"
)
ui
<-
function
(
request
)
{
fluidPage
(
useShinyjs
(),
titlePanel
(
"Two Proportion Resampling Test"
),
sidebarLayout
(
sidebarPanel
(
tabsetPanel
(
tabPanel
(
"Test"
,
tags
$
div
(
class
=
"header"
,
checked
=
NA
,
tags
$
p
(
"Enter your data into the table
below, or choose one of the data
presets. Press the Shuffle button
to simulate the results under an
independence null model."
)
),
hr
(),
selectInput
(
inputId
=
"plot"
,
label
=
"Plot Type"
,
choices
=
c
(
"Dotplot"
,
"Histogram"
)),
selectInput
(
inputId
=
"presets"
,
label
=
"Presets"
,
selected
=
"Custom"
,
# selects the initial preset
choices
=
names
(
Presets
)),
html_table
,
actionButton
(
inputId
=
"Reset"
,
label
=
"Reset"
),
numericInput
(
inputId
=
"numsamp"
,
label
=
"Shuffle how many times?"
,
value
=
100
,
min
=
1
,
max
=
5000
),
tags
$
div
(
class
=
"header"
,
checked
=
NA
,
tags
$
p
(
"Enter a value from 1 to 5000"
)),
actionButton
(
"Replicate"
,
"Shuffle"
)
),
tabPanel
(
"Information"
,
tags
$
div
(
class
=
"header"
,
checked
=
NA
,
tags
$
p
(
"Enter the value of your observed difference of proportions in the text
under the graph. Selecting 'greater/less than' will highlight the
samples that are greater/less than your value."
),
tags
$
p
(
"Selecting 'beyond' will highlight the samples that are further away
from 0 than your value."
),
tags
$
p
(
"Press the Reset button whenever you change the values in the table."
),
hr
(),
hr
(),
tags
$
p
(
"Written by Scott Manski"
),
tags
$
p
(
"This work is licensed under a "
),
tags
$
a
(
href
=
"http://creativecommons.org/licenses/by-sa/4.0/"
,
"Creative Commons Attribution-ShareAlike 4.0 International License"
),
hr
(),
bookmarkButton
()
)
))),
mainPanel
(
plotOutput
(
"RandomPlot"
),
checkboxInput
(
"Show.Observed"
,
"Show observed difference"
,
FALSE
),
textOutput
(
"Observed.Diff"
),
fluidRow
(
column
(
textOutput
(
"count.samples"
),
width
=
3
),
column
(
selectInput
(
"inequality"
,
NULL
,
c
(
"greater than"
,
"less than"
,
"beyond"
)),
width
=
3
),
column
(
textInput
(
"cutoff"
,
NULL
),
width
=
4
),
htmlOutput
(
"counts"
))
)
)
)}
server
<-
function
(
input
,
output
,
session
)
{
# initialize values for use in server
values
<-
reactiveValues
()
values
$
props
<-
vector
()
values
$
table
<-
matrix
(
rep
(
NA
,
9
),
ncol
=
3
)
# colors for plots
values
$
hist.fill.color
<-
"grey70"
# histogram bar fill color
values
$
hist.outline.color
<-
"black"
# histogram bar outline color
values
$
dot.fill.color
<-
"grey70"
# dotplot dot fill color
values
$
cutoff.color
<-
"#F05133"
# color for cutoff values
# observe any changes in table
observe
({
values
$
table
[
1
,
1
]
<-
as.numeric
(
input
$
TL
)
# top left position
values
$
table
[
1
,
2
]
<-
as.numeric
(
input
$
TR
)
# top right position
values
$
table
[
2
,
1
]
<-
as.numeric
(
input
$
BL
)
# bottom left position
values
$
table
[
2
,
2
]
<-
as.numeric
(
input
$
BR
)
# bottom right position
values
$
table
[
1
,
3
]
<-
as.numeric
(
input
$
TL
)
+
as.numeric
(
input
$
TR
)
#top sum
values
$
table
[
2
,
3
]
<-
as.numeric
(
input
$
BL
)
+
as.numeric
(
input
$
BR
)
# bottom sum
values
$
table
[
3
,
1
]
<-
as.numeric
(
input
$
TL
)
+
as.numeric
(
input
$
BL
)
# left sum
values
$
table
[
3
,
2
]
<-
as.numeric
(
input
$
TR
)
+
as.numeric
(
input
$
BR
)
# right sum
values
$
table
[
3
,
3
]
<-
as.numeric
(
input
$
TL
)
+
as.numeric
(
input
$
TR
)
+
# total sum
as.numeric
(
input
$
BL
)
+
as.numeric
(
input
$
BR
)
# calculates the limits for the plots based on the standard deviation
# the standard deviation is calculated based on the Hypergeometric distribution
values
$
x.lim
<-
6
*
sqrt
(
values
$
table
[
3
,
1
]
*
values
$
table
[
1
,
3
]
/
values
$
table
[
3
,
3
]
*
values
$
table
[
2
,
3
]
/
values
$
table
[
3
,
3
]
*
values
$
table
[
3
,
2
]
/
(
values
$
table
[
3
,
3
]
-1
)
/
values
$
table
[
1
,
3
]
^
2
+
values
$
table
[
3
,
2
]
*
values
$
table
[
2
,
3
]
/
values
$
table
[
3
,
3
]
*
values
$
table
[
1
,
3
]
/
values
$
table
[
3
,
3
]
*
values
$
table
[
3
,
1
]
/
(
values
$
table
[
3
,
3
]
-1
)
/
values
$
table
[
2
,
3
]
^
2
)
})
# output for values of table if there is a change
output
$
TRT
<-
renderText
({
values
$
table
[
1
,
3
]
})
output
$
TRB
<-
renderText
({
values
$
table
[
2
,
3
]
})
output
$
TBL
<-
renderText
({
values
$
table
[
3
,
1
]
})
output
$
TBR
<-
renderText
({
values
$
table
[
3
,
2
]
})
output
$
Total
<-
renderText
({
values
$
table
[
3
,
3
]
})
# these will update each time the user clicks the Replicate button
observeEvent
(
input
$
Replicate
||
input
$
Show.Observed
,
{
values
$
observed
<-
values
$
table
[
1
,
1
]
/
values
$
table
[
1
,
3
]
-
values
$
table
[
2
,
1
]
/
values
$
table
[
2
,
3
]
})
# reset the values if "Reset" is pressed
observeEvent
(
input
$
Reset
,
{
values
$
props
<-
vector
()
enable
(
"Replicate"
)
})
# checks to see if the current table matches a preset, otherwise the preset is "Custom"
observeEvent
(
c
(
input
$
TL
,
input
$
TR
,
input
$
BL
,
input
$
BR
,
input
$
C1N
,
input
$
C2N
,
input
$
R1N
,
input
$
R2N
),
{
# combine the current table inputs into a vector
current
<-
c
(
input
$
TL
,
input
$
BL
,
input
$
TR
,
input
$
BR
,
input
$
C1N
,
input
$
C2N
,
input
$
R1N
,
input
$
R2N
)
# loops through each preset and determines the number of cells that match the current table
preset
<-
unlist
(
lapply
(
names
(
Presets
),
function
(
i
)
{
sum
(
Presets
[[
i
]]
==
current
)
}))
# if all cells match, change the SelectInput value to that preset,
# otherwise change the value to "Custom"
if
(
sum
(
preset
==
8
)
>
0
)
{
updateSelectInput
(
session
,
"presets"
,
selected
=
names
(
Presets
)[
which
(
preset
==
8
)])
}
else
{
updateSelectInput
(
session
,
"presets"
,
selected
=
"Custom"
)
}
},
ignoreInit
=
TRUE
)
# disable or enable the "Shuffle" button
# the "Shuffle" button in enabled when the number of shuffles is less than
# 5,000 and the total number of shuffles is less than 20,000
observeEvent
(
input
$
numsamp
,
{
if
(
is.numeric
(
input
$
numsamp
)){
if
(
input
$
numsamp
>
5000
){
disable
(
"Replicate"
)
}
else
if
(
length
(
values
$
props
)
<=
20000
){
enable
(
"Replicate"
)
}
}
})
# update the values when shuffle is pressed
observeEvent
(
input
$
Replicate
,
{
new.vals
<-
rhyper
(
input
$
numsamp
,
values
$
table
[
1
,
3
],
values
$
table
[
2
,
3
],
values
$
table
[
3
,
1
])
new.vals
<-
new.vals
/
values
$
table
[
1
,
3
]
-
(
values
$
table
[
3
,
1
]
-
new.vals
)
/
values
$
table
[
2
,
3
]
values
$
props
<-
c
(
values
$
props
,
new.vals
)
if
(
length
(
values
$
props
)
>=
20000
){
disable
(
"Replicate"
)
}
else
{
enable
(
"Replicate"
)
}
},
ignoreInit
=
TRUE
)
# when "Beyond" is selected, this function is used to calculate the probability
# for each possible outcome.
two_sided_values
<-
function
()
{
m
<-
values
$
table
[
1
,
3
]
n
<-
values
$
table
[
2
,
3
]
k
<-
values
$
table
[
3
,
1
]
support
<-
c
(
max
(
0
,
k
-
n
)
:
min
(
k
,
m
))
x
<-
dhyper
(
support
,
m
,
n
,
k
)
names
(
x
)
<-
support
x
}
# update the counts for the cutoff if there are any changes
update_counts
<-
eventReactive
(
c
(
input
$
cutoff
,
input
$
Replicate
,
input
$
Reset
,
input
$
inequality
,
input
$
presets
),
{
if
(
!
is.na
(
as.numeric
(
input
$
cutoff
))){
# the error is used to handle rounded values of input$cutoff
num.decimals
<-
decimalcount
(
as.character
(
input
$
cutoff
))
error
<-
ifelse
(
num.decimals
<=
1
,
0
,
0.1
^
num.decimals
/
2
)
# for "greater than", finds the number and proportion of values greater than
# input$cutoff - error. For "less than", finds the number and proportion of
# values less than input$cutoff + error. For beyond, the number and proportion
# of values is calculated by adding up all points such that the probability of
# obtaining that point is less than or equal to that of input$cutoff see
# https://en.wikipedia.org/wiki/Fisher%27s_exact_test, the second to last paragraph
# in the Example section)
if
(
input
$
inequality
==
"greater than"
){
values
$
prob
<-
sum
(
values
$
props
>=
as.numeric
(
input
$
cutoff
)
-
error
)
/
length
(
values
$
props
)
values
$
count
<-
sum
(
values
$
props
>=
as.numeric
(
input
$
cutoff
)
-
error
)
}
else
if
(
input
$
inequality
==
"less than"
)
{
values
$
prob
<-
sum
(
values
$
props
<=
as.numeric
(
input
$
cutoff
)
+
error
)
/
length
(
values
$
props
)
values
$
count
<-
sum
(
as.numeric
(
values
$
props
)
<=
as.numeric
(
input
$
cutoff
)
+
error
)
}
else
{
x
<-
two_sided_values
()
cutoff
<-
x
[
which
(
names
(
x
)
==
values
$
table
[
1
,
1
])]
vals
<-
as.numeric
(
names
(
x
)[
which
(
x
<=
cutoff
)])
vals
<-
vals
/
values
$
table
[
1
,
3
]
-
(
values
$
table
[
3
,
1
]
-
vals
)
/
values
$
table
[
2
,
3
]
values
$
prob
<-
length
(
which
(
values
$
props
%in%
vals
))
/
length
(
values
$
props
)
values
$
count
<-
length
(
which
(
values
$
props
%in%
vals
))
}
}
})
# creates the desired plot
output
$
RandomPlot
<-
renderPlot
({
if
(
length
(
values
$
props
)
!=
0
&
!
is.na
(
values
$
table
[
3
,
1
])){
# after reset, values$props is empty
DF
<-
values
$
table
if
(
input
$
plot
==
"Dotplot"
){
# plot == TRUE is dotplot, FALSE is histogram
# n is the number of columns for the dotplot
# large datasets will have n <- 1
if
(
DF
[
3
,
1
]
>
1000
){
n
<-
1
}
else
{
n
<-
4
}
# gets the dotplot locations for the dotplot
df
<-
dotplot_locs
(
values
$
props
,
n
,
input
$
cutoff
,
values
$
cutoff.color
,
values
$
dot.fill.color
,
input
$
inequality
)
df
<-
df
[
df
$
x
<
values
$
x.lim
&
df
$
x
>
-
values
$
x.lim
,
]
myplot
<-
ggplot
(
df
)
+
geom_point
(
aes
(
x
,
y
,
colour
=
fill.color
),
size
=
min
(
n
,
50
/
length
(
values
$
props
)
^
0.5
))
+
scale_colour_manual
(
name
=
"fill.color"
,
values
=
levels
(
df
$
fill.color
))
+
scale_y_continuous
(
limits
=
c
(
0
,
max
(
n
*
7.5
,
max
(
df
$
y
))))
+
scale_x_continuous
(
limits
=
c
(
-
values
$
x.lim
,
values
$
x.lim
))
+
labs
(
x
=
"Shuffled Difference in Proportions"
,
y
=
"Count"
)
+
plaintheme
+
axistheme
}
else
{
df
<-
data.frame
(
"x"
=
values
$
props
[
values
$
props
<
values
$
x.lim
&
values
$
props
>
-
values
$
x.lim
])
unique.vals
<-
sort
(
unique
(
as.numeric
(
as.character
(
df
$
x
))))
# a histogram is created to determine the bars that need to be colored
myplot
<-
ggplot
(
df
,
aes
(
x
=
x
))
+
geom_histogram
(
binwidth
=
max
(
diff
(
unique.vals
)))
+
scale_x_continuous
(
limits
=
c
(
-
values
$
x.lim
,
values
$
x.lim
))
names.counts
<-
ggplot_build
(
myplot
)
$
data
[[
1
]]
$
x
# color is determined if input$cutoff is specified
if
(
!
is.na
(
as.numeric
(
input
$
cutoff
))){
num.decimals
<-
decimalcount
(
as.character
(
input
$
cutoff
))
error
<-
ifelse
(
num.decimals
<=
2
,
0
,
0.1
^
num.decimals
/
2
)
if
(
input
$
inequality
==
"greater than"
){
to.color
<-
which
(
names.counts
>=
as.numeric
(
input
$
cutoff
)
-
error
)
}
else
if
(
input
$
inequality
==
"less than"
){
to.color
<-
which
(
names.counts
<=
as.numeric
(
input
$
cutoff
)
+
error
)
}
else
{
to.color
<-
c
(
which
(
names.counts
<=
-1
*
abs
(
as.numeric
(
input
$
cutoff
))
+
error
),
which
(
names.counts
>=
abs
(
as.numeric
(
input
$
cutoff
))
-
error
))
}
}
else
{
to.color
<-
NA
}
fill.color
<-
rep
(
values
$
hist.fill.color
,
length
(
names.counts
))
fill.color
[
to.color
]
<-
values
$
cutoff.color
# the histogram is plotted
myplot
<-
ggplot
(
df
,
aes
(
x
=
x
))
+
geom_histogram
(
binwidth
=
max
(
diff
(
unique.vals
)),
fill
=
fill.color
,
col
=
values
$
hist.outline.color
)
+
labs
(
x
=
"Shuffled Difference in Proportions"
,
y
=
"Count"
)
+
scale_x_continuous
(
limits
=
c
(
-
values
$
x.lim
,
values
$
x.lim
))
+
plaintheme
+
axistheme
}
myplot
}
})
# calculate the observed difference when checkbox is TRUE
output
$
Observed.Diff
<-
renderText
({
if
(
input
$
Show.Observed
){
DF
<-
data
()
values
$
observed
=
values
$
table
[
1
,
1
]
/
values
$
table
[
1
,
3
]
-
values
$
table
[
2
,
1
]
/
values
$
table
[
2
,
3
]
paste
(
"Observed Difference:"
,
round
(
values
$
observed
,
6
))
}
})
# text for sample counts
output
$
count.samples
<-
renderText
({
"Count Samples"
})
# output for counts when cutoff is specified
output
$
counts
<-
renderText
({
update_counts
()
if
(
!
is.null
(
values
$
prob
)){
if
(
is.na
(
values
$
prob
)){
" "
}
else
if
(
!
is.na
(
as.numeric
(
input
$
cutoff
))){
paste
(
"<font color="
,
values
$
cutoff.color
,
"><b>"
,
values
$
count
,
"/"
,
length
(
values
$
props
),
" ("
,
round
(
values
$
prob
,
4
),
")"
,
"</b></font>"
,
sep
=
""
)
}
else
if
(
nchar
(
input
$
cutoff
)
!=
0
){
"<font color=\"#FF0000\"><b>Invalid Cutoff!</b></font>"
}
else
{
" "
}
}
})
# changes table if a different preset is selected
observeEvent
(
input
$
presets
,
{
values
$
props
<-
vector
()
enable
(
"Replicate"
)
if
(
input
$
presets
!=
"Custom"
)
{
preset_index
<-
which
(
names
(
Presets
)
==
input
$
presets
)
preset
<-
Presets
[[
preset_index
]]
DF
<-
data.frame
(
"X1"
=
as.numeric
(
preset
[
1
:
2
]),
"X2"
=
as.numeric
(
preset
[
3
:
4
]))
DF
[
3
,
]
<-
apply
(
DF
,
2
,
sum
)
DF
[,
3
]
<-
apply
(
DF
,
1
,
sum
)
values
$
table
<-
DF
values
$
table.names
<-
preset
[
5
:
8
]
updateTextInput
(
session
,
"TL"
,
value
=
values
$
table
[
1
,
1
])
updateTextInput
(
session
,
"TR"
,
value
=
values
$
table
[
1
,
2
])
updateTextInput
(
session
,
"BL"
,
value
=
values
$
table
[
2
,
1
])
updateTextInput
(
session
,
"BR"
,
value
=
values
$
table
[
2
,
2
])
updateTextInput
(
session
,
"C1N"
,
value
=
values
$
table.names
[
1
])
updateTextInput
(
session
,
"C2N"
,
value
=
values
$
table.names
[
2
])
updateTextInput
(
session
,
"R1N"
,
value
=
values
$
table.names
[
3
])
updateTextInput
(
session
,
"R2N"
,
value
=
values
$
table.names
[
4
])
}
})
## Bookmarking ##
# to remove bookmarking, remove bookmarkButton() from the ui
# when the bookmark button is pressed, the current values of props and table are saved
onBookmark
(
function
(
state
)
{
state
$
values
$
props
<-
values
$
props
state
$
values
$
table
<-
values
$
table
})
# when opening a bookmarked page, props is restored
onRestored
(
function
(
state
)
{
values
$
props
<-
state
$
values
$
props
})
# when opening a bookmarked page, table is restored
onRestore
(
function
(
state
)
{
values
$
table
<-
state
$
values
$
table
})
}
shinyApp
(
ui
=
ui
,
server
=
server
,
options
=
list
(
height
=
1080
),
enableBookmarking
=
"server"
)
\ No newline at end of file
This diff is collapsed.
Click to expand it.
TwoProportionResamplingTest/TwoProportionSource.R
0 → 100644
+
182
−
0
View file @
1d263249
# HTML code for editable table
html_table
<-
HTML
(
"<script type='text/javascript'>
/*<![CDATA[*/
function Expand1(){
if (!R1N.savesize) R1N.savesize=R1N.size;
if (!R2N.savesize) R2N.savesize=R2N.size;
var isChrome = !!window.chrome && (!!window.chrome.webstore || !!window.chrome.runtime);
var isSafari = /constructor/i.test(window.HTMLElement) || (function (p) { return p.toString() === '[object SafariRemoteNotification]'; })(!window['safari'] || (typeof safari !== 'undefined' && safari.pushNotification));
var isIE = /*@cc_on!@*/false || !!document.documentMode;
offset = 0;
if (isSafari) offset = 3;
R1N.size=Math.max(R1N.savesize,R1N.value.length,R2N.value.length)-offset;
R2N.size=Math.max(R2N.savesize,R1N.value.length,R2N.value.length)-offset;
}
function Expand2(){
if (!C1N.savesize) C1N.savesize=C1N.size;
if (!TL.savesize) TL.savesize=TL.size;
if (!BL.savesize) BL.savesize=BL.size;
var isChrome = !!window.chrome && (!!window.chrome.webstore || !!window.chrome.runtime);
var isSafari = /constructor/i.test(window.HTMLElement) || (function (p) { return p.toString() === '[object SafariRemoteNotification]'; })(!window['safari'] || (typeof safari !== 'undefined' && safari.pushNotification));
var isIE = /*@cc_on!@*/false || !!document.documentMode;
offset = 0;
if (isSafari) offset = 3;
C1N.size=Math.max(C1N.savesize,C1N.value.length,TL.value.length,BL.value.length)-offset;
TL.size=Math.max(TL.savesize,C1N.value.length,TL.value.length,BL.value.length)-offset;
BL.size=Math.max(BL.savesize,C1N.value.length,TL.value.length,BL.value.length)-offset;
}
function Expand3(){
if (!C2N.savesize) C2N.savesize=C2N.size;
if (!TR.savesize) TR.savesize=TR.size;
if (!BR.savesize) BR.savesize=BR.size;
var isChrome = !!window.chrome && (!!window.chrome.webstore || !!window.chrome.runtime);
var isSafari = /constructor/i.test(window.HTMLElement) || (function (p) { return p.toString() === '[object SafariRemoteNotification]'; })(!window['safari'] || (typeof safari !== 'undefined' && safari.pushNotification));
var isIE = /*@cc_on!@*/false || !!document.documentMode;
offset = 0;
if (isSafari) offset = 3;
C2N.size=Math.max(C2N.savesize,C2N.value.length,TR.value.length,BR.value.length)-offset;
TR.size=Math.max(TR.savesize,C2N.value.length,TR.value.length,BR.value.length)-offset;
BR.size=Math.max(BR.savesize,C2N.value.length,TR.value.length,BR.value.length)-offset;
}
/*]]>*/
</script><style>
table{
border-color: #f3f7fb;
display: block;
overflow-x: auto;
}
th, td {
border: 1px solid black;
border-collapse: collapse;
padding: 6px;
}
input {
border: 0;
width: auto;
padding: 1px 8px;
background-color: #f5f5f5;
font-size: 1em;
}
</style>
<table id = 'mytable'>
<tbody>
<tr>
<td></td>
<td><input size='1' id='C1N'type = 'text' onchange='Expand2();' oninput='Expand2();' value='Column A'></td>
<td><input size='1' id='C2N'type = 'text' onchange='Expand3();' oninput='Expand3();' value='Column B'></td>
<td><div style='padding: 1px 8px'>Total</div></td>
</tr>
<tr>
<td><input size='1' id='R1N'type = 'text' onchange='Expand1();' oninput='Expand1();' value='Row 1'></td>
<td><input size='1' id='TL' type='text' onchange='Expand2();' oninput='Expand2();' value='0'></td>
<td><input size='1' id='TR' type = 'text' onchange='Expand3();' oninput='Expand3();' value='0'></td>
<td><div size='1' style='padding: 1px 8px' id='TRT' class='shiny-text-output'></div></td>
</tr>
<tr>
<td><input size='1' id='R2N' type = 'text' onchange='Expand1();' oninput='Expand1();' value='Row 2'></td>
<td><input size='1' id='BL' type = 'text' onchange='Expand2();' oninput='Expand2();' value='0'></td>
<td><input size='1' id='BR' type = 'text' onchange='Expand3();' oninput='Expand3();' value='0'></td>
<td><div size='1' style='padding: 1px 8px' id='TRB' class='shiny-text-output'></div></td>
</tr>
<tr>
<td><div style='padding: 1px 8px'>Total</div></td>
<td><div size='1' style='padding: 1px 8px' id='TBL' class='shiny-text-output'></div></td>
<td><div size='1' style='padding: 1px 8px' id='TBR' class='shiny-text-output'></div></td>
<td><div size='1' style='padding: 1px 8px' id='Total' class='shiny-text-output'></div></td>
</tr>
</tbody>
</table>"
)
# determines the number of decimal places of a number
decimalcount
<-
function
(
x
){
stopifnot
(
class
(
x
)
==
"character"
)
x
<-
gsub
(
"(.*)(\\.)|([0]*$)"
,
""
,
x
)
as.numeric
(
nchar
(
x
))
}
# create dotplot locations from data x
dotplot_locs
<-
function
(
x
,
n
,
cutoff
,
cutoff.color
,
dot.fill.color
,
inequality
){
counts
<-
table
(
x
)
x.locs
<-
as.numeric
(
names
(
counts
))
# find minimum difference between points, with an exeption for a single point
if
(
length
(
names
(
counts
))
==
1
){
point_dist
<-
min
(
diff
(
c
(
0
,
as.numeric
(
names
(
counts
)))))
/
(
n
+2
)
}
else
{
point_dist
<-
min
(
diff
(
as.numeric
(
names
(
counts
))))
/
(
n
+2
)
}
# define the standard x coordinates to be used
x.coord
<-
sapply
(
x.locs
,
function
(
x
)
x
+
((
1
:
n
)
-
(
n
+1
)
/
2
)
*
point_dist
)
x.coords
<-
vector
()
y.coords
<-
vector
()
to.color
<-
vector
()
names.counts
<-
as.numeric
(
names
(
counts
))
# loop through each count, defining new x and y coordinates for "dotplot"
for
(
i
in
1
:
length
(
counts
)){
if
(
n
==
1
){
x.coords
<-
c
(
x.coords
,
rep
(
x.coord
[
i
],
counts
[
i
]
/
n
))
}
else
{
x.coords
<-
c
(
x.coords
,
rep
(
x.coord
[,
i
],
counts
[
i
]
/
n
),
x.coord
[
0
:
(
counts
[
i
]
%%
n
),
i
])
}
if
(
counts
[
i
]
>
n
){
y.coords
<-
c
(
y.coords
,
sort
(
rep
(
1
:
(
counts
[
i
]
/
n
),
n
)),
rep
(
ceiling
(
counts
[
i
]
/
n
),
counts
[
i
]
%%
n
))
}
else
{
y.coords
<-
c
(
y.coords
,
sort
(
rep
(
1
:
(
counts
[
i
]
/
n
),
counts
[
i
])))
}
# defines color of dots when cutoff defined
if
(
!
is.na
(
as.numeric
(
cutoff
))){
num.decimals
<-
decimalcount
(
as.character
(
cutoff
))
# error term for rounded cutoff values
error
<-
ifelse
(
num.decimals
<=
2
,
0
,
0.1
^
num.decimals
/
2
)
if
(
inequality
==
"greater than"
){
if
(
names.counts
[
i
]
>=
as.numeric
(
cutoff
)
-
error
){
to.color
<-
c
(
to.color
,
rep
(
cutoff.color
,
counts
[
i
]))
}
else
{
to.color
<-
c
(
to.color
,
rep
(
dot.fill.color
,
counts
[
i
]))
}
}
else
if
(
inequality
==
"less than"
)
{
if
(
names.counts
[
i
]
<=
as.numeric
(
cutoff
)
+
error
){
to.color
<-
c
(
to.color
,
rep
(
cutoff.color
,
counts
[
i
]))
}
else
{
to.color
<-
c
(
to.color
,
rep
(
dot.fill.color
,
counts
[
i
]))
}
}
else
{
if
((
names.counts
[
i
]
<=
-1
*
abs
(
as.numeric
(
cutoff
))
+
error
)
|
(
names.counts
[
i
]
>=
abs
(
as.numeric
(
cutoff
))
-
error
)){
to.color
<-
c
(
to.color
,
rep
(
cutoff.color
,
counts
[
i
]))
}
else
{
to.color
<-
c
(
to.color
,
rep
(
dot.fill.color
,
counts
[
i
]))
}
}
}
else
{
to.color
<-
c
(
to.color
,
rep
(
dot.fill.color
,
counts
[
i
]))
}
}
return
(
data.frame
(
"x"
=
x.coords
,
"y"
=
y.coords
*
n
,
"fill.color"
=
to.color
))
}
# theme for plots
plaintheme
<-
theme_bw
()
+
theme
(
plot.background
=
element_blank
(),
panel.grid.major
=
element_blank
(),
panel.grid.minor
=
element_blank
()
)
+
theme
(
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
1
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
1
))
+
theme
(
legend.position
=
"none"
,
plot.margin
=
margin
(
10
,
10
,
10
,
10
))
# axis theme for plots
axistheme
<-
theme
(
plot.title
=
element_text
(
hjust
=
0.5
,
color
=
"black"
,
face
=
"bold"
,
size
=
20
))
+
theme
(
axis.title
=
element_text
(
color
=
"black"
,
size
=
16
))
+
theme
(
axis.text.x
=
element_text
(
size
=
14
,
color
=
"black"
))
+
theme
(
axis.text.y
=
element_text
(
size
=
14
,
color
=
"black"
))
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