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plotly for design sample
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@deril2605
deril2605 committed Apr 19, 2024
1 parent db2013a commit 7862798
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, Normalization
LazyData: true
URL: http://msstats.org
BugReports: https://groups.google.com/forum/#!forum/msstats
RoxygenNote: 7.3.0
RoxygenNote: 7.3.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2017-10-20 02:13:12 UTC; meenachoi
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130 changes: 99 additions & 31 deletions R/designSampleSize.R
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Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,9 @@ designSampleSize = function(
#' (4) power. The input is the result from function (\code{\link{designSampleSize}}.
#'
#' @param data output from function designSampleSize.
#' @param isPlotly Parameter to use Plotly or ggplot2. If set to TRUE, MSstats
#' will save Plotly plots as HTML files. If set to FALSE MSstats will save ggplot2 plots
#' as PDF files
#'
#' @details Data in the example is based on the results of sample size calculation from function \code{\link{designSampleSize}}
#'
Expand Down Expand Up @@ -246,7 +249,7 @@ designSampleSize = function(
#' desiredFC=c(1.25,1.75), FDR=0.05, power=TRUE)
#' designSampleSizePlots(data=result.power)
#'
designSampleSizePlots = function(data) {
designSampleSizePlots = function(data, isPlotly = FALSE) {
if (length(unique(data$numSample)) > 1) {
index = "numSample"
} else if (length(unique(data$power)) > 1) {
Expand All @@ -257,39 +260,104 @@ designSampleSizePlots = function(data) {
stop ("Invalid input")
}

text.size = 1.2
axis.size = 1.3
lab.size = 1.7

if(isPlotly) {
axis.size <- 10
lab.size <- 12
text.size <- 12
} else {
text.size = 1.2
axis.size = 1.3
lab.size = 1.7
}
if (index == "numSample") {
plot(data$desiredFC, data$numSample,
lwd=2, xlab="", ylab="",
cex.axis=axis.size, type="l", xaxt="n")
axis(1, at=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
labels=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
cex.axis=axis.size)
mtext("Desired fold change", 1, line=3.5, cex=lab.size)
mtext("Minimal number of biological replicates", 2, line=2.5, cex=lab.size)
legend("topright",
c(paste("FDR is", unique(data$FDR)),
paste("Statistical power is", unique(data$power))),
bty="n",
cex=text.size)
if(isPlotly) {
p <- plot_ly(data, x = ~desiredFC, y = ~numSample, type = 'scatter', mode = 'lines',
line = list(width = 2)) %>%
layout(
xaxis = list(
title = "Desired fold change",
tickvals = seq(min(data$desiredFC), max(data$desiredFC), 0.05),
ticktext = seq(min(data$desiredFC), max(data$desiredFC), 0.05),
tickfont = list(size = axis.size)
),
yaxis = list(
title = "Minimal number of biological replicates",
tickfont = list(size = axis.size)
),
annotations = list(
list(
x = 1, y = 1, xref = 'paper', yref = 'paper',
text = sprintf("FDR is %s<br>Statistical power is %s",
paste(unique(data$FDR), collapse = ", "),
paste(unique(data$power), collapse = ", ")),
showarrow = FALSE,
xanchor = 'right', yanchor = 'top',
font = list(size = text.size)
)
),
margin = list(t = 50) # Adjust top margin to avoid cutting off text
)
return(p)
}
else {
plot(data$desiredFC, data$numSample,
lwd=2, xlab="", ylab="",
cex.axis=axis.size, type="l", xaxt="n")
axis(1, at=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
labels=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
cex.axis=axis.size)
mtext("Desired fold change", 1, line=3.5, cex=lab.size)
mtext("Minimal number of biological replicates", 2, line=2.5, cex=lab.size)
legend("topright",
c(paste("FDR is", unique(data$FDR)),
paste("Statistical power is", unique(data$power))),
bty="n",
cex=text.size)
}
}

if (index == "power") {
plot(data$desiredFC, data$power,
lwd=2, xlab="", ylab="",
cex.axis=axis.size, type="l", xaxt="n")
axis(1, at=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
labels=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
cex.axis=axis.size)
mtext("Desired fold change", 1, line=3.5, cex=lab.size)
mtext("Power", 2, line=2.5, cex=lab.size)
legend("bottomright",
c(paste("Number of replicates is", unique(data$numSample)),
paste("FDR is", unique(data$FDR))),
bty="n",
cex=text.size)
if(isPlotly) {
p <- plot_ly(data, x = ~desiredFC, y = ~power, type = 'scatter', mode = 'lines',
line = list(width = 2)) %>%
layout(
xaxis = list(
title = "Desired fold change",
tickvals = seq(min(data$desiredFC), max(data$desiredFC), 0.05),
ticktext = seq(min(data$desiredFC), max(data$desiredFC), 0.05),
tickfont = list(size = axis.size)
),
yaxis = list(
title = "Power",
tickfont = list(size = axis.size)
),
showlegend = FALSE, # Hide default legend
annotations = list(
list(
x = 0.5, y = 0.5, xref = 'paper', yref = 'paper',
text = paste("Number of replicates is", unique(data$numSample), "<br>FDR is", unique(data$FDR)),
showarrow = FALSE,
xanchor = 'right', yanchor = 'bottom',
font = list(size = text.size)
)
),
margin = list(b = 100) # Adjust bottom margin if necessary
)
return(p)
} else {
plot(data$desiredFC, data$power,
lwd=2, xlab="", ylab="",
cex.axis=axis.size, type="l", xaxt="n")
axis(1, at=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
labels=seq(min(data$desiredFC), max(data$desiredFC), 0.05),
cex.axis=axis.size)
mtext("Desired fold change", 1, line=3.5, cex=lab.size)
mtext("Power", 2, line=2.5, cex=lab.size)
legend("bottomright",
c(paste("Number of replicates is", unique(data$numSample)),
paste("FDR is", unique(data$FDR))),
bty="n",
cex=text.size)
}
}
}
6 changes: 5 additions & 1 deletion man/designSampleSizePlots.Rd
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