added file for plots

Author: alysiaymk

R/data_frame_selection.R

@@ -4,12 +4,15 @@ library(psd)
 library(mFilter)
 library(ggplot2)
 library(data.table)
+library(plotly)
 source("~/Documents/snail_back_pack/R/funs.R")
 DATA_FILE <- "/home/alysia/Documents/snail_back_pack/R/ref_data_heart_snail.txt"
 REF_FILE <- "/home/alysia/Documents/ref.csv"
-SAMPLING_FREQ <- 5 # in Hz
 
+SAMPLING_FREQ <- 5 # in Hz
 
+DATA_FILE <- "/home/alysia/Documents/heart_021.csv"
+REF_FILE <- "/home/alysia/Documents/snail_back_pack/experiments/snail_minute_slices/snail_21minute.csv"
 
 
 
@@ -41,16 +44,6 @@ lapply(list_of_mins, function(l){
 dev.off()
 
 
-pdf("/tmp/proto_plot.pdf",w=16,h=9)
-sapply(result21, function(l){
-	y <- l["freq"]
-	t0 <- l["tmin"][1]
-	title <- paste("pspec_bwfilter;", t0)
-	freq_fun_pspec_bwfilter(y, fs=5, dev=T, main=title)
-	})
-dev.off()
-
-
 pdf("plot.pdf",w=16,h=9)
 lapply(list_of_mins, function(sdf){
 		title <- sdf$min[1]
@@ -62,9 +55,9 @@ dev.off()
 #list of results from methods and ggplot generation
 results <- list(
 
-	meth_pspec = apply_freq_meth(chunk=list_of_mins, freq_fun_pspec, fs=5),
-	meth_pspec_bwfilter = apply_freq_meth(chunks=list_of_mins, freq_fun_pspec_bwfilter, fs=5),
-	meth_pspec_runmed = apply_freq_meth(chunk=list_of_mins, freq_fun_pspec_runmed, fs=5, k=43)
+	#pspec = apply_freq_meth(chunk=list_of_mins, freq_fun_pspec, fs=5)
+	pspec_bwfilter = apply_freq_meth(chunks=list_of_mins, freq_fun_pspec_bwfilter, fs=5),
+	pspec_runmed = apply_freq_meth(chunk=list_of_mins, freq_fun_pspec_runmed, fs=5, k=43)
 	)
 
 

R/funs.R

@@ -56,7 +56,7 @@ freq_fun_pspec_runmed <- function(y, fs, k){
 
 #generates original spectra and filtered spectra
 freq_fun_bwfilter <- function(y, fs, dev=TRUE,...){
-	bwf <- bwfilter(y,freq=4,drift=TRUE)
+	bwf <- bwfilter(y,freq=3,drift=TRUE)
 
 	if(dev == T){
 		plot(y,type="l",...)
@@ -67,7 +67,7 @@ freq_fun_bwfilter <- function(y, fs, dev=TRUE,...){
 
 #generates, original spectra, power spectrum, and fpeaks
 freq_fun_pspec_bwfilter <- function(y, fs, dev=TRUE,...){
-	bwf <- bwfilter(y,freq=78,drift=TRUE)
+	bwf <- bwfilter(y,freq=3,drift=TRUE)
 	pspec_test <- pspectrum(bwf$trend, x.frqsamp=fs)
 	f <- seewave::fpeaks(pspec_test$spec, f=fs,nmax=1, plot=T, title=F)
 	if(any(is.na(f))){
@@ -100,6 +100,27 @@ freq_fun_pspec_bwfilter_runmed <- function(y, fs, k, dev=TRUE,...){
 	return(f[1,1]*1000)
 }
 
+#freq_fun_pspec_iirfilter_pspec<- function(y, fs, k, dev=TRUE,...){
+
+	#pspec_test <- pspectrum(bwf$trend, x.frqsamp=fs)
+	#f <- seewave::fpeaks(pspec_test$spec, f=fs,nmax=1, plot=T, title=F)
+	#if(any(is.na(f))){
+	#	return(.0 + NA)
+	#	}
+	
+	#return(f[1,1]*1000)
+#}
+
+
+
+#f1 <- iir(sines, fl = 0.5, fh = 1.5, type = "BP", proto = "BU")
+#lines(f1, col = "blue")
+
+
+
+
+
+
 apply_freq_meth <- function(chunks, FUN, fs, ...){
 	sapply(chunks, function(d, fs, ... ){ 
 		FUN(d$y, fs, ...)

R/plots.R

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+py <- plotly()
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+model <- lm(fc ~ reof + factor(method), data=long_df)
+grid <- with(long_df, expand.grid(
+  reof = seq(min(reof), max(reof), length = 3),
+  method = levels(factor(method))
+))
+
+grid$fc <- stats::predict(model, newdata=grid)
+
+viz2 <- qplot(reof, fc, data=long_df, colour=factor(method)) + 
+geom_line(data=grid)
+out <- py$ggplotly(viz2, kwargs=list(filename="gg-line-scatter", fileopt="overwrite"))
+plotly_url <- out$response$url
+
+
+
+py <- plotly()
+
+model <- lm(mpg ~ wt + factor(cyl), data=mtcars)
+grid <- with(mtcars, expand.grid(
+  wt = seq(min(wt), max(wt), length = 20),
+  cyl = levels(factor(cyl))
+))
+
+grid$mpg <- stats::predict(model, newdata=grid)
+
+viz2 <- qplot(wt, mpg, data=mtcars, colour=factor(cyl)) +
+            geom_line(data=grid)
+out <- py$ggplotly(viz2, kwargs=list(filename="gg-line-scatter", fileopt="overwrite"))
+plotly_url <- out$response$url
+
+
+
+
+pltpspec <- ggplot(long_df,aes(y = fc, x =reof,colour=method,shape=method)) +
+	geom_point() + geom_smooth(method="lm", fill=NA) + 
+	coord_cartesian(xlim = c(0, xmax+0.25), ylim = c(0, ymax+0.25)) +
+	geom_abline(group=1, colour="grey")
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