Demo Web App for Calcium Imaging Time-Lapse Series Analysis
This is a demo app that would crush if you attempted to analyse more than four frames. For larger series analysis, download code at GitHub (click) . Running a code as a Shiny app would require e.g. Rstudio.
Generation of Correlation Heatmaps Online
If Pearson's correlation is done after "detrending" (removal of a linear trend) the dataset the negative values are often generated. The app coverts all the negatives into to NaNs (Not-a-Number"). p
Detrending is done using the following R language expression and it uses multiple breaking points (bp)
br <- 50 #breaking point
break.points <- seq(from=br,to=dim(dat2)[1], by=br)
dat3 <- dat2 #imported data stored in dat2
for(i in 1:dim(dat2)[2]){ # run each Sample in a dataframe in a loop
dat3[,i] <- detrend(dat2[,i], bp=break.points) # detrend the data
};
dat3[,1] <- dat2[,1] ## This line replaces detrended "Time" column with original values
The users have an option to chose heatmaps from a R package - pheatmap, which generate blue to yellow to red palette. Or from a package gplot - heatmap.2. The latter one uses yellow to red color scheme as default. Useres could chose e.g. bluered or greenred (spelled as a single word) palette.
Users can also calculate the persentage of the correlating pairs, out of the total number of all possible pairs in the sample. Finally, one can calculate all datapoints above a certain threshold (default is zero), evaluating e.g. sample's overall activity
Video instructions
on how to make a scatter plot overlayed with column graphs online
How to Make a Grouped Graph Combined with Scatter Plot Online
How to Make Stacked Bar Charts Online. How to Generate Percent Stacked Bar Charts on the web