diff --git a/R/designSampleSize.R b/R/designSampleSize.R
index abc950f..2cb469e 100644
--- a/R/designSampleSize.R
+++ b/R/designSampleSize.R
@@ -272,31 +272,29 @@ designSampleSizePlots = function(data, isPlotly = FALSE) {
if (index == "numSample") {
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
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
+ line = list(width = 2))
+ p <- layout(p, 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
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 {
@@ -319,30 +317,28 @@ designSampleSizePlots = function(data, isPlotly = FALSE) {
if (index == "power") {
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$numSample), "
FDR is", unique(data$FDR)),
- showarrow = FALSE,
- xanchor = 'right', yanchor = 'bottom',
- font = list(size = text.size)
- )
- ),
- margin = list(b = 100) # Adjust bottom margin if necessary
+ line = list(width = 2))
+ p <- layout(p, 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$numSample), "
FDR is", unique(data$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,