diff --git a/NEWS.md b/NEWS.md index b8a62e8d..31f2e98d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,7 +7,7 @@ #### Other changes -* Made some minor improvements to the vignette. +* Made some minor changes to vignette to improve clarity (e.g. using single wavelength for integration, etc.) #### Bug fixes diff --git a/vignettes/chromatographR.Rmd b/vignettes/chromatographR.Rmd index f9e6893d..2433170c 100644 --- a/vignettes/chromatographR.Rmd +++ b/vignettes/chromatographR.Rmd @@ -97,11 +97,11 @@ oldpar <- par(no.readonly = TRUE) # save current par settings par(mfrow=c(2,1)) # plot warped data -plot_chroms(warp, lambdas = c("210","260")) +plot_chroms(warp, lambdas = c("210")) legend("topleft", legend="ptw", bty = "n") # plot unwarped data -plot_chroms(dat.pr, lambdas = c("210","260")) +plot_chroms(dat.pr, lambdas = c("210")) legend("topleft", legend="raw", bty = "n") par(oldpar) # restore par settings ``` @@ -121,10 +121,10 @@ warp <- correct_rt(chrom_list = dat.pr, alg = "vpdtw", lambdas = "210", what = " oldpar <- par(no.readonly = TRUE) # save current par settings par(mfrow=c(2,1)) -plot_chroms(warp, lambdas = c("210","260")) +plot_chroms(warp, lambdas = c("210")) legend("topleft", legend = "vpdtw", bty = "n") -plot_chroms(dat.pr, lambdas = c("210","260")) +plot_chroms(dat.pr, lambdas = c("210")) legend("topleft", legend = "raw", bty = "n") par(oldpar) # restore par settings @@ -138,13 +138,13 @@ The `get_peaks` function produced a nested list of peaks by looping through the ```{r get_peaks, message=FALSE, warning=FALSE} # find and integrate peaks using gaussian peak fitting -pks_gauss <- get_peaks(warp, lambdas = c('210','260'), sd.max = 40, fit = "gaussian") +pks_gauss <- get_peaks(warp, lambdas = c('210'), sd.max = 40, fit = "gaussian") # find and integrate peaks using exponential-gaussian hybrid model -pks_egh <- get_peaks(warp, lambdas = c('210', '260'), sd.max = 40, fit="egh") +pks_egh <- get_peaks(warp, lambdas = c('210'), sd.max = 40, fit="egh") # find and integrate peaks without modeling peak shape -pks_raw <- get_peaks(warp, lambdas = c('210', '260'), sd.max = 100, fit="raw") +pks_raw <- get_peaks(warp, lambdas = c('210'), sd.max = 100, fit="raw") ``` #### Filtering @@ -199,7 +199,7 @@ pk_tab <- normalize_data(peak_table = pk_tab, column="mass") The `mirror_plot` function provides a quick way to visually compare results across treatment groups. ```{r mirror_plot} -mirror_plot(pk_tab, lambdas = c("210","260"), var = "trt", legend_size = 2) +mirror_plot(pk_tab, lambdas = c("210"), var = "trt", legend_size = 2) ``` ##### Plotting spectra