Skip to content

GitLab

Commit 1b6761f1 authored by Amine GHOZLANE's avatar Amine GHOZLANE
Browse files
Options

Solved issue with missing data in diversities

parent d82b7044
Pipeline #15935 passed with stage
    in 8 minutes and 18 seconds
    Hide whitespace changes
    Inline Side-by-side
    Showing with 20 additions and 16 deletions
    Rfunctions/VisuPlot.R
    View file @ 1b6761f1
    ......@@ -446,32 +446,36 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE, alpha_transparen
    #save(counts_tmp_combined,targetInt,file = "testDiv.RData")
    alpha <- tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, mean)
    alpha=alpha[!is.na(alpha)]
    alpha_selected = !is.na(alpha)
    alpha=alpha[alpha_selected]
    alpha_sd = tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, sd)
    alpha_sd=alpha_sd[!is.na(alpha_sd)]
    ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb,0)
    ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb
    alpha_sd=alpha_sd[alpha_selected]
    ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb[alpha_selected],0)
    ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb[alpha_selected]
    shan <- tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, mean)
    shan = shan[!is.na(shan)]
    shan_selected = !is.na(shan)
    shan = shan[shan_selected]
    shan_sd = tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, sd)
    shan_sd = shan_sd[!is.na(shan_sd)]
    ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb,0)
    ci.shan.up = shan + 1.96*shan_sd/sqrt.nb
    shan_sd = shan_sd[shan_selected]
    ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb[shan_selected],0)
    ci.shan.up = shan + 1.96*shan_sd/sqrt.nb[shan_selected]
    simpson <- tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, mean)
    simpson = simpson[!is.na(simpson)]
    simpson_selected = !is.na(simpson)
    simpson = simpson[simpson_selected]
    simpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, sd)
    simpson_sd = simpson_sd[!is.na(simpson_sd)]
    ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb,0)
    ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb
    simpson_sd = simpson_sd[simpson_selected]
    ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb[simpson_selected],0)
    ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb[simpson_selected]
    invsimpson <- tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, mean)
    invsimpson = invsimpson[!is.na(invsimpson)]
    invsimpson_selected = !is.na(invsimpson)
    invsimpson = invsimpson[invsimpson_selected]
    invsimpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, sd)
    invsimpson_sd = invsimpson_sd[!is.na(invsimpson_sd)]
    ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb,0)
    ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb
    invsimpson_sd = invsimpson_sd[invsimpson_selected]
    ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected],0)
    ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected]
    gamma <- TaxoNumber(counts_tmp_combined, targetInt$AllVar)
    gamma = gamma[!is.na(gamma)]
    ......
    Markdown is supported
    0% or .
    You are about to add 0 people to the discussion. Proceed with caution.
    Finish editing this message first!
    Please register or to comment