plot_con_effectsize: plot_con_effectsize

In LyonsZhang/ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries

Usage

plot_con_effectsize(bestoutputs, variable, testdata, estitle = NULL, saveesfile, espicdim, crtitle = NULL, savecrfile, crpicdim, goodtype = "goodpvname", effecttext = FALSE)

Arguments

bestoutputs
variable
testdata
estitle
saveesfile
espicdim
crtitle
savecrfile
crpicdim
goodtype
effecttext

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (bestoutputs, variable, testdata, estitle = NULL, saveesfile, 
    espicdim, crtitle = NULL, savecrfile, crpicdim, goodtype = "goodpvname", 
    effecttext = FALSE) 
{
    select <- switch(goodtype, goodpsigname = bestoutputs$goodpsigname, 
        goodpvname = bestoutputs$goodpvname, goodesname = bestoutputs$goodesname, 
        goodcrname = bestoutputs$goodcrname, stop("goodtype must be one of the follows: 'goodpsigname', 'goodpvname', 'goodesname' and 'goodcrname'. "))
    selname <- bestoutputs$selname
    df <- data.frame(matrix(0, length(selname), 2))
    row.names(df) <- selname
    colnames(df) <- c("selname", "effectsize")
    df$selname <- selname
    df$effectsize <- bestoutputs$effectsize0
    df1 <- df[selname %in% select, ]
    df1$signed <- sign(df1$effectsize)
    temp <- df1[df1$signed == -1, ]
    temp <- temp[order(temp$effectsize), ]
    df1 <- rbind(df1[df1$signed == 1, ], temp)
    df1$selname <- factor(df1$selname, levels = df1$selname)
    df1[[variable]] <- factor(ifelse(df1$signed == 1, "positive", 
        "negative"))
    p <- ggplot(df1, aes(selname, effectsize)) + geom_bar(stat = "identity", 
        aes_string(fill = variable)) + scale_fill_manual(values = c("#00b0f6", 
        "#f8766d")) + geom_hline(yintercept = 0, size = 2) + 
        ylab("Effect size") + xlab("Selected features with decreasing order") + 
        coord_flip() + ggtitle(estitle) + theme_bw() + theme(plot.title = element_text(size = 30, 
        face = "bold"), legend.title = element_text(size = 20), 
        legend.text = element_text(size = 16)) + theme(axis.line = element_line(colour = "black"), 
        panel.border = element_blank(), panel.background = element_blank(), 
        axis.line.x = element_line(color = "black", size = 1), 
        axis.line.y = element_line(color = "black", size = 1), 
        axis.text = element_text(size = 16, face = "bold"), axis.title = element_text(size = 20, 
            face = "bold"))
    if (effecttext == TRUE) {
        p <- p + geom_text(aes(label = round(effectsize, 2), 
            hjust = 0.5, angle = 0))
    }
    p
    ggsave(filename = saveesfile, width = espicdim[1], height = espicdim[2])
    df <- data.frame(matrix(0, length(selname), 2))
    row.names(df) <- selname
    colnames(df) <- c("selname", "correlation")
    df$selname <- selname
    df$correlation <- bestoutputs$correlation0
    df2 <- df[selname %in% select, ]
    df2$signed <- sign(df2$correlation)
    temp <- df2[df2$signed == -1, ]
    temp <- temp[order(temp$correlation), ]
    df2 <- rbind(df2[df2$signed == 1, ], temp)
    df2$selname <- factor(df2$selname, levels = df2$selname)
    df2[[variable]] <- factor(ifelse(df2$signed == 1, "positive", 
        "negative"))
    p <- ggplot(df2, aes(selname, correlation)) + geom_bar(stat = "identity", 
        aes_string(fill = variable)) + scale_fill_manual(values = c("#00b0f6", 
        "#f8766d")) + geom_hline(yintercept = 0, size = 2) + 
        ylab("Correlation") + xlab("Selected features with decreasing order") + 
        coord_flip() + ggtitle(crtitle) + theme_bw() + theme(plot.title = element_text(size = 30, 
        face = "bold"), legend.title = element_text(size = 20), 
        legend.text = element_text(size = 16)) + theme(axis.line = element_line(colour = "black"), 
        panel.border = element_blank(), panel.background = element_blank(), 
        axis.line.x = element_line(color = "black", size = 1), 
        axis.line.y = element_line(color = "black", size = 1), 
        axis.text = element_text(size = 16, face = "bold"), axis.title = element_text(size = 20, 
            face = "bold"))
    if (effecttext == TRUE) {
        p <- p + geom_text(aes(label = round(correlation, 2), 
            hjust = 0.5, angle = 0))
    }
    p
    ggsave(filename = savecrfile, width = crpicdim[1], height = crpicdim[2])
    return(list(sigeffectsize = df1, sigcorrelation = df2))
  }

LyonsZhang/ProgPermute documentation built on July 22, 2020, 4:09 p.m.