plot_TS: Plot G-BLUEs time series data
In ICRISAT-GEMS/SpaTemHTP: Processing and utilization of HTP data

Description Usage Arguments Details Value Author(s) See Also Examples

Plot G-BLUEs time series data.

1	plot_TS(data_TS, trend = NULL, h2 = NULL, TW_lim = NULL, main = "G-BLUEs TS")

`data_TS`	`numeric` `matrix` of dimension N_genotype x N_days containing the phenotype information. the different columns represent the different time points (e.g. days, hours) of measurement.
`trend`	Optional `numeric` `matrix` of dimension n_days containing the values of the trend to be ploted on the top of the time series Default = NULL.
`h2`	Optional heritability `numeric vector` that will be used to indicate the day with the highest heritability. Default = NULL.
`TW_lim`	Optional time window limits `numeric vector` that will be used to indicate the time window limit days. Those values can be obtained with `cpa_getOTW_2`. Default = NULL.
`main`	`Character` string representing the title of the graph. Default = 'G-BLUEs TS'.

The function plots the times series data of phenotyping data per genotype replicate or averaged over genotype replicate using the ggplot2 package.

Plot of the G-BLUEs time series. The optional trend will be ploted in red. The heritability will be ploted in dashed blue and time window limits in black.

Soumyashree Kar, Vincent Garin

SpaTemHTP_proc

data(SG_PH_data)
data <- SG_PH_data
geno_id <- data$genotype

g_means <- matrix(NA, 384, 23)

for(i in 1:23){
  
  g_av <- tapply(X = data[, i + 5], INDEX = geno_id,
                 FUN = function(x) mean(x, na.rm = TRUE))
  g_means[, i] <- g_av
  
}

rownames(g_means) <- names(g_av)

plot_TS(data_TS = g_means, main = 'Raw data genotype means')