quantp: quantp.r annotate

annotate quantp.r @ 1:bcc7a4c4cc29 draft

planemo upload commit 1887dff812162880d66b003a927867cd5000c98f

author	galaxyp
date	Thu, 20 Dec 2018 16:06:05 -0500
parents	75faf9a89f5b
children	ed0bb50d7ffe

rev	line source
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	2 # Functions: Start
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	3 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	4
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	5 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	6 # PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	7 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	8 multisample_PCA = function(df, sampleinfo_df, outfile)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	9 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	10 tempdf = df[,-1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	11 tempcol = colnames(tempdf);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	12 tempgrp = sampleinfo_df[tempcol,2];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	13 tempdf = t(tempdf) %>% as.data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	14 tempdf[is.na(tempdf)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	15 tempdf$Group = tempgrp;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	16 png(outfile, width = 6, height = 6, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	17 # bitmap(outfile, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	18 g = autoplot(prcomp(select(tempdf, -Group)), data = tempdf, colour = 'Group', size=3);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	19 saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outplot)))
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	20 plot(g);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	21 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	22 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	23
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	24 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	25 # Regression and Cook's distance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	26 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	27 singlesample_regression = function(PE_TE_data,htmloutfile, append=TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	28 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	29 rownames(PE_TE_data) = PE_TE_data$PE_ID;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	30 regmodel = lm(PE_abundance~TE_abundance, data=PE_TE_data);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	31 regmodel_summary = summary(regmodel);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	32
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	33 cat("<font><h3>Linear Regression model fit between Proteome and Transcriptome data</h3></font>\n",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	34 "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	35 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	36 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	37
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	38 cat("<tr><td>Formula</td><td>","PE_abundance~TE_abundance","</td></tr>\n",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	39 "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	40 "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	41 "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	42 "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	43 "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	44 "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	45 "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	46 "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	47 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	48
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	49 cat("</table>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	50
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	51 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	52 "<font color='#ff0000'><h3>Regression and diagnostics plots</h3></font>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	53 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	54
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	55 outplot = paste(outdir,"/PE_TE_lm_1.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	56 png(outplot, width = 10, height = 10, units = 'in',res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	57 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	58 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	59 plot(regmodel, 1, cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	60 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	61
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	62 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[1]] +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	63 geom_point(aes(text=sprintf("Residual: %.2f<br>Fitted value: %.2f<br>Gene: %s", .fitted, .resid, PE_TE_data$PE_ID)),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	64 shape = 1, size = .1, stroke = .2) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	65 theme_light())
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	66 saveWidget(ggplotly(g, tooltip= c("text")), file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	67
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	68 outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	69 png(outplot,width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	70 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	71 par(mfrow=c(1,1));
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	72 g <- plot(regmodel, 2, cex.lab=1.5);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	73 ggplotly(g)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	74 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	75
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	76 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[2]] +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	77 geom_point(aes(text=sprintf("Standarized residual: %.2f<br>Theoretical quantile: %.2f<br>Gene: %s", .qqx, .qqy, PE_TE_data$PE_ID)),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	78 shape = 1, size = .1) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	79 theme_light())
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	80 saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	81
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	82
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	83 outplot = paste(outdir,"/PE_TE_lm_5.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	84 png(outplot, width = 10, height = 10, units = 'in',res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	85 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	86 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	87 plot(regmodel, 5, cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	88 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	89
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	90 cd_cont_pos <- function(leverage, level, model) {sqrt(levellength(coef(model))(1-leverage)/leverage)}
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	91 cd_cont_neg <- function(leverage, level, model) {-cd_cont_pos(leverage, level, model)}
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	92
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	93 suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[4]] +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	94 aes(label = PE_TE_data$PE_ID) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	95 geom_point(aes(text=sprintf("Leverage: %.2f<br>Standardized residual: %.2f<br>Gene: %s", .hat, .stdresid, PE_TE_data$PE_ID))) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	96 theme_light())
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	97 saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	98
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	99 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	100
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	101 cat(
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	102 '<tr bgcolor="#7a0019"><th>', "<font color='#ffcc33'><h4>1) <u>Residuals vs Fitted plot</h4></font></u></th>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	103 '<th><font color=#ffcc33><h4>2) <u>Normal Q-Q plot of residuals</h4></font></u></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	104 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	105
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	106 cat(
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	107 '<tr><td align=center><img src="PE_TE_lm_1.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	108 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$widget_div),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	109 '</td><td align=center><img src="PE_TE_lm_2.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	110 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$widget_div),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	111 '</td></tr>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	112
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	113 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	114 '<tr><td align=center>This plot checks for linear relationship assumptions.<br>If a horizontal line is observed without any distinct patterns, it indicates a linear relationship.</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	115 '<td align=center>This plot checks whether residuals are normally distributed or not.<br>It is good if the residuals points follow the straight dashed line i.e., do not deviate much from dashed line.</td></tr></table>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	116 file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	117
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	118
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	119 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	120 # Residuals data
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	121 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	122 res_all = regmodel$residuals;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	123 res_mean = mean(res_all);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	124 res_sd = sd(res_all);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	125 res_diff = (res_all-res_mean);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	126 res_zscore = res_diff/res_sd;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	127 # res_outliers = res_all[which((res_zscore > 2)\|(res_zscore < -2))]
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	128
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	129
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	130 tempind = which((res_zscore > 2)\|(res_zscore < -2));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	131 res_PE_TE_data_no_outlier = PE_TE_data[-tempind,];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	132 res_PE_TE_data_no_outlier$residuals = res_all[-tempind];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	133 res_PE_TE_data_outlier = PE_TE_data[tempind,];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	134 res_PE_TE_data_outlier$residuals = res_all[tempind];
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	135
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	136 # Save the complete table for download (influential_observations)
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	137 temp_outlier_data = data.frame(res_PE_TE_data_outlier$PE_ID, res_PE_TE_data_outlier$TE_abundance, res_PE_TE_data_outlier$PE_abundance, res_PE_TE_data_outlier$residuals)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	138 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	139 outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	140 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	141
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	142
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	143 # Save the complete table for download (non influential_observations)
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	144 temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	145 colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	146 outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	147 write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	148
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	149
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	150 cat('<br><h2 id="inf_obs"><font color=#ff0000>Outliers based on the residuals from regression analysis</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	151 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	152 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	153 '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	154 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	155 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	156
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	157 cat("<tr><td>Mean Residual value</td><td>",res_mean,"</td></tr>\n",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	158 "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	159 '<tr><td>Total outliers (Residual value > 2 standard deviation from the mean)</td><td>',length(tempind),' <font size=4>(<b><a href="PE_TE_outliers_residuals.txt" target="_blank">Download these ',length(tempind),' data points with high residual values here</a></b>)</font></td>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	160 '<tr><td colspan=2 align=center>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	161 '<font size=4>(<b><a href="PE_TE_abundance_residuals.txt" target="_blank">Download the complete residuals data here</a></b>)</font>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	162 "</td></tr>\n</table><br><br>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	163 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	164
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	165 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	166
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	167
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	168 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	169
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	170 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	171 '<tr bgcolor="#7a0019"><th><font color=#ffcc33><h4>3) <u>Residuals vs Leverage plot</h4></font></u></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	172 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	173
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	174 cat(
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	175 '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	176 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$widget_div)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	177 , '</td></tr>\n',
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	178 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	179
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	180 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	181 '<tr><td align=center>This plot is useful to identify any influential cases, that is outliers or extreme values.<br>They might influence the regression results upon inclusion or exclusion from the analysis.</td></tr></table><br>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	182 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	183
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	184
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	185
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	186 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	187 # Cook's Distance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	188 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	189 cat('<hr/><h2 id="inf_obs"><font color=#ff0000>INFLUENTIAL OBSERVATIONS</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	190 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	191 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	192 '<p><b>Cook\'s distance</b> computes the influence of each data point/observation on the predicted outcome. i.e. this measures how much the observation is influencing the fitted values.<br>In general use, those observations that have a <b>Cook\'s distance > than ', cookdist_upper_cutoff,' times the mean</b> may be classified as <b>influential.</b></p>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	193 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	194
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	195 cooksd <- cooks.distance(regmodel);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	196
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	197 outplot = paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	198 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	199 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	200 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	201 plot(cooksd, main="Influential Obs. by Cook\'s distance", ylab="Cook\'s distance", xlab="Observations", type="n") # plot cooks distance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	202 sel_outlier=which(cooksd>=as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	203 sel_nonoutlier=which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	204 points(sel_outlier, cooksd[sel_outlier],pch="*", cex=2, cex.lab=1.5, col="red")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	205 points(sel_nonoutlier, cooksd[sel_nonoutlier],pch="*", cex=2, cex.lab=1.5, col="black")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	206 abline(h = as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T), col="red") # add cutoff line
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	207 #text(x=1:length(cooksd)+1, y=cooksd, labels=ifelse(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T),names(cooksd),""), col="red", pos=2) # add labels
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	208 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	209
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	210 cooksd_df <- data.frame(cooksd)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	211 cooksd_df$genes <- row.names(cooksd_df)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	212 cooksd_df$index <- 1:nrow(cooksd_df)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	213 cooksd_df$colors <- "black"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	214 cutoff <- as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	215 cooksd_df[cooksd_df$cooksd > cutoff,]$colors <- "red"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	216
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	217 g <- ggplot(cooksd_df, aes(x = index, y = cooksd, label = row.names(cooksd_df), color=as.factor(colors),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	218 text=sprintf("Gene: %s<br>Cook's Distance: %.3f", row.names(cooksd_df), cooksd))) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	219 ggtitle("Influential Obs. by Cook's distance") + xlab("Observations") + ylab("Cook's Distance") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	220 #xlim(0, 3000) + ylim(0, .15) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	221 scale_shape_discrete(solid=F) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	222 geom_point(size = 2, shape = 8) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	223 geom_hline(yintercept = cutoff,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	224 linetype = "dashed", color = "red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	225 scale_color_manual(values = c("black" = "black", "red" = "red")) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	226 theme_light() + theme(legend.position="none")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	227 saveWidget(ggplotly(g, tooltip= "text"), file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	228
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	229 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	230 '<img src="PE_TE_lm_cooksd.png" width=800 height=800>',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	231 gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div),
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	232 '<br>In the above plot, observations above red line (',cookdist_upper_cutoff,' * mean Cook\'s distance) are influential. Genes that are outliers could be important. These observations influences the correlation values and regression coefficients<br><br>',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	233 file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	234
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	235 tempind = which(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	236 PE_TE_data_no_outlier = PE_TE_data[-tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	237 PE_TE_data_no_outlier$cooksd = cooksd[-tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	238 PE_TE_data_outlier = PE_TE_data[tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	239 PE_TE_data_outlier$cooksd = cooksd[tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	240 a = sort(PE_TE_data_outlier$cooksd, decreasing=T, index.return=T);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	241 PE_TE_data_outlier_sorted = PE_TE_data_outlier[a$ix,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	242
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	243 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	244 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	245 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	246
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	247 # Save the complete table for download (influential_observations)
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	248 temp_outlier_data = data.frame(PE_TE_data_outlier$PE_ID, PE_TE_data_outlier$TE_abundance, PE_TE_data_outlier$PE_abundance, PE_TE_data_outlier$cooksd)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	249 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	250 outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	251 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	252
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	253
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	254 # Save the complete table for download (non influential_observations)
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	255 temp_no_outlier_data = data.frame(PE_TE_data_no_outlier$PE_ID, PE_TE_data_no_outlier$TE_abundance, PE_TE_data_no_outlier$PE_abundance, PE_TE_data_no_outlier$cooksd)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	256 colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	257 outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	258 write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	259
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	260
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	261 cat("<tr><td>Mean Cook\'s distance</td><td>",mean(cooksd, na.rm=T),"</td></tr>\n",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	262 "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	263
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	264 "<tr><td>Observations with Cook\'s distance < ",cookdist_upper_cutoff," * mean Cook\'s distance</td><td>",length(which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))),"</td>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	265 "</table><br><br>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	266 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	267
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	268
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	269 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	270 # Scatter plot after removal of influential points
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	271 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	272 outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	273 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	274 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	275 png(outplot, width = 10, height = 10, units = 'in', res=300);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	276 # bitmap(outplot,"png16m");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	277 suppressWarnings(g <- ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	278 xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	279 xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	280 geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	281 PE_ID, TE_abundance, PE_abundance))))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	282 suppressMessages(plot(g))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	283 suppressMessages(saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot))))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	284 dev.off();
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	285
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	286
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	287 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatterplot: Before removal</font></th><th><font color=#ffcc33>Scatterplot: After removal</font></th></tr>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	288 # Before
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	289 cat("<tr><td align=center><!--<font color='#ff0000'><h3>Scatter plot between Proteome and Transcriptome Abundance</h3></font>\n-->",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	290 '<img src="TE_PE_scatter.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	291 gsub('id="html', 'id="secondhtml"',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	292 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$widget_div)),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	293 '</td>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	294 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	295
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	296 # After
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	297 cat("<td align=center>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	298 '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	299 gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(outplot)$widget_div),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	300
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	301 '</td></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	302 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	303 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	304
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	305
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	306 cor_result_pearson = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "pearson");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	307 cor_result_spearman = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "spearman");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	308 cor_result_kendall = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "kendall");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	309
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	310 cat('<tr><td>\n', file = htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	311 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	312 cat('</td>\n', file = htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	313
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	314
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	315 cat('<td><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Method 1</font></th><th><font color=#ffcc33>Method 2</font></th><th><font color=#ffcc33>Method 3</font></th></tr>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	316 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	317
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	318 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	319 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	320 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$estimate,"</td><td>",cor_result_spearman$estimate,"</td><td>",cor_result_kendall$estimate,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	321 file = htmloutfile, append = TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	322 cat("</table></td></tr></table>\n", file = htmloutfile, append = TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	323
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	324
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	325
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	326 if(dim(PE_TE_data_outlier)[1]<10)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	327 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	328 tab_n_row = dim(PE_TE_data_outlier)[1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	329 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	330 tab_n_row = 10;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	331 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	332
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	333 cat("<br><br><font size=5><b><a href='PE_TE_influential_observation.txt' target='_blank'>Download the complete list of influential observations</a></b></font>    ",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	334 "<font size=5><b><a href='PE_TE_non_influential_observation.txt' target='_blank'>Download the complete list (After removing influential points)</a></b></font><br>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	335 '<br><font color="brown"><h4>Top ',as.character(tab_n_row),' Influential observations (Cook\'s distance > ',cookdist_upper_cutoff,' * mean Cook\'s distance)</h4></font>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	336 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	337
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	338 cat('<table border=1 cellspacing=0 cellpadding=5> <tr bgcolor="#7a0019">\n', sep = "",file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	339 cat("<th><font color=#ffcc33>Gene</font></th><th><font color=#ffcc33>Protein Log Fold-Change</font></th><th><font color=#ffcc33>Transcript Log Fold-Change</font></th><th><font color=#ffcc33>Cook's Distance</font></th></tr>\n",
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	340 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	341
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	342
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	343 for(i in 1:tab_n_row)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	344 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	345 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	346 '<tr>','<td>',as.character(PE_TE_data_outlier_sorted[i,1]),'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	347 '<td>',format(PE_TE_data_outlier_sorted[i,2], scientific=F),'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	348 '<td>',PE_TE_data_outlier_sorted[i,4],'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	349 '<td>',format(PE_TE_data_outlier_sorted[i,5], scientific=F),'</td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	350 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	351 }
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	352 cat('</table><br><br>\n',file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	353
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	354
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	355 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	356
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	357
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	358
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	359 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	360 # Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	361 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	362 singlesample_heatmap=function(PE_TE_data, htmloutfile, hm_nclust){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	363 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Heatmap of PE and TE abundance values (Hierarchical clustering)</font></th><th><font color=#ffcc33>Number of clusters to extract: ',hm_nclust,'</font></th></tr>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	364 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	365
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	366 hc=hclust(dist(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")])))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	367 hm_cluster = cutree(hc,k=hm_nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	368
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	369 outplot = paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	370 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	371 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	372 par(mfrow=c(1,1));
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	373 hmap = heatmap.2(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	374 trace="none", cexCol=1, col=greenred(100),Colv=F,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	375 labCol=c("Proteins","Transcripts"), scale="col",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	376 hclustfun = hclust, distfun = dist);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	377
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	378 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	379
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	380
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	381 p <- d3heatmap(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]), scale = "col",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	382 dendrogram = "row", colors = greenred(100),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	383 hclustfun = hclust, distfun = dist,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	384 show_grid = FALSE)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	385 saveWidget(p, file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	386
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	387 cat('<tr><td align=center colspan="2">',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	388 '<img src="PE_TE_heatmap.png" width=800 height=800>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	389 gsub("width:960px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	390 '</td></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	391 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	392
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	393
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	394 temp_PE_TE_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, hm_cluster);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	395 colnames(temp_PE_TE_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cluster (Hierarchical clustering)")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	396 tempoutfile = paste(outdir,"/PE_TE_hc_clusterpoints.txt",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	397 write.table(temp_PE_TE_data, file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	398
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	399
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	400 cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_hc_clusterpoints.txt" target="_blank"><b>Download the hierarchical cluster list</b></a></font></td></tr></table>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	401 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	402 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	403
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	404
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	405 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	406 # K-means clustering
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	407 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	408 singlesample_kmeans=function(PE_TE_data, htmloutfile, nclust){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	409 PE_TE_data_kdata = PE_TE_data;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	410 k1 = kmeans(PE_TE_data_kdata[,c("PE_abundance","TE_abundance")], nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	411 outplot = paste(outdir,"/PE_TE_kmeans.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	412 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	413 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	414 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	415 scatter.smooth(PE_TE_data_kdata[,"TE_abundance"], PE_TE_data_kdata[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	416 legend(1, 95, legend=c("Cluster 1", "Line 2"), col="red", lty=1:1, cex=0.8)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	417 legend(1, 95, legend="Cluster 2", col="green", lty=1:1, cex=0.8)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	418
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	419 ind=which(k1$cluster==1);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	420 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="red", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	421 ind=which(k1$cluster==2);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	422 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="green", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	423 ind=which(k1$cluster==3);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	424 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="blue", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	425 ind=which(k1$cluster==4);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	426 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="cyan", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	427 ind=which(k1$cluster==5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	428 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="black", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	429 ind=which(k1$cluster==6);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	430 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="brown", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	431 ind=which(k1$cluster==7);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	432 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="gold", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	433 ind=which(k1$cluster==8);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	434 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="thistle", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	435 ind=which(k1$cluster==9);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	436 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="yellow", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	437 ind=which(k1$cluster==10);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	438 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="orange", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	439 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	440
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	441 # Interactive plot for k-means clustering
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	442 g <- ggplot(PE_TE_data, aes(x = TE_abundance, y = PE_abundance, label = row.names(PE_TE_data),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	443 text=sprintf("Gene: %s<br>Transcript Abundance: %.3f<br>Protein Abundance: %.3f",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	444 PE_ID, TE_abundance, PE_abundance),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	445 color=as.factor(k1$cluster))) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	446 xlab("Transcript Abundance") + ylab("Protein Abundance") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	447 scale_shape_discrete(solid=F) + geom_smooth(method = "loess", span = 2/3) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	448 geom_point(size = 1, shape = 8) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	449 theme_light() + theme(legend.position="none")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	450 saveWidget(ggplotly(g, tooltip=c("text")), file.path(gsub("\\.png", "\\.html", outplot)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	451
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	452 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>K-mean clustering</font></th><th><font color=#ffcc33>Number of clusters: ',nclust,'</font></th></tr>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	453 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	454
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	455 tempind = order(k1$cluster);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	456 tempoutfile = paste(outdir,"/PE_TE_kmeans_clusterpoints.txt",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	457 write.table(data.frame(PE_TE_data_kdata[tempind, ], Cluster=k1$cluster[tempind]), file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	458
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	459 #paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	460 cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	461 gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div), '</td></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	462 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	463 cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_kmeans_clusterpoints.txt" target="_blank"><b>Download the cluster list</b></a></font></td></tr></table><br><hr/>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	464 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	465
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	466 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	467
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	468 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	469 # scatter plot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	470 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	471 singlesample_scatter = function(PE_TE_data, outfile)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	472 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	473 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	474 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	475 png(outfile, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	476 # bitmap(outfile, "png16m");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	477 suppressWarnings(g <- ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	478 xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	479 xlim(min_lim,max_lim) + ylim(min_lim,max_lim) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	480 geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	481 PE_ID, TE_abundance, PE_abundance)),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	482 size = .5))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	483 suppressMessages(plot(g))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	484 suppressMessages(saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outfile))))
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	485 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	486 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	487
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	488 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	489 # Correlation table
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	490 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	491 singlesample_cor = function(PE_TE_data, htmloutfile, append=TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	492 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	493 cor_result_pearson = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "pearson");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	494 cor_result_spearman = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "spearman");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	495 cor_result_kendall = cor.test(PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, method = "kendall");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	496
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	497 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	498 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Method 1</font></th><th><font color=#ffcc33>Method 2</font></th><th><font color=#ffcc33>Method 3</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	499 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	500
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	501 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	502 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	503 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$estimate,"</td><td>",cor_result_spearman$estimate,"</td><td>",cor_result_kendall$estimate,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	504 file = htmloutfile, append = TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	505 cat("</table>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	506
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	507 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	508
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	509 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	510 # Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	511 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	512 multisample_boxplot = function(df, sampleinfo_df, outfile, fill_leg, user_xlab, user_ylab)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	513 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	514 tempdf = df[,-1, drop=FALSE];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	515 tempdf = t(tempdf) %>% as.data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	516 tempdf[is.na(tempdf)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	517 tempdf$Sample = rownames(tempdf);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	518 tempdf1 = melt(tempdf, id.vars = "Sample");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	519
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	520 if("Gene" %in% colnames(df)){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	521 tempdf1$Name = df$Gene;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	522 } else if ("Protein" %in% colnames(df)){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	523 tempdf1$Name = df$Protein;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	524 } else if ("Genes" %in% colnames(df)){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	525 tempdf1$Name = df$Genes;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	526 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	527
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	528 tempdf1$Group = sampleinfo_df[tempdf1$Sample,2];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	529 png(outplot, width = 6, height = 6, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	530 # bitmap(outplot, "png16m");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	531 if(fill_leg=="No"){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	532 tempdf1$Group = c("case", "control")
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	533 }
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	534
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	535 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	536 geom_boxplot()+
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	537 labs(x=user_xlab) + labs(y=user_ylab)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	538 saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outfile)))
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	539 plot(g);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	540 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	541 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	542
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	543 ## A wrapper to saveWidget which compensates for arguable BUG in
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	544 ## saveWidget which requires `file` to be in current working
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	545 ## directory.
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	546 saveWidget <- function (widget,file,...) {
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	547 wd<-getwd()
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	548 on.exit(setwd(wd))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	549 outDir<-dirname(file)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	550 file<-basename(file)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	551 setwd(outDir);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	552 htmlwidgets::saveWidget(widget,file=file,selfcontained = FALSE)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	553 }
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	554
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	555 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	556 # Mean or Median of Replicates
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	557 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	558
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	559 mergeReplicates = function(TE_df,PE_df, sampleinfo_df, method)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	560 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	561 grps = unique(sampleinfo_df[,2]);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	562
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	563 TE_df_merged <<- sapply(grps, function(x){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	564 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	565 if(length(tempsample)!=1){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	566 apply(TE_df[,tempsample],1,method);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	567 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	568 return(TE_df[,tempsample]);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	569 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	570 });
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	571 TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	572 colnames(TE_df_merged) = c(colnames(TE_df)[1], grps);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	573
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	574 PE_df_merged <<- sapply(grps, function(x){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	575 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	576 if(length(tempsample)!=1){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	577 apply(PE_df[,tempsample],1,method);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	578 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	579 return(PE_df[,tempsample]);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	580 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	581 });
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	582
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	583 PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	584 colnames(PE_df_merged) = c(colnames(PE_df)[1], grps);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	585
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	586 #sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	587 sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	588
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	589 return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged));
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	590 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	591
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	592 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	593 # (T-Test or Wilcoxon ranksum test) and Volcano Plot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	594 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	595
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	596 perform_Test_Volcano = function(TE_df_data,PE_df_data,TE_df_logfold, PE_df_logfold,sampleinfo_df, method, correction_method,volc_with)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	597 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	598
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	599 PE_colnames = colnames(PE_df_data);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	600 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	601 control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	602 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	603 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	604
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	605 if(method=="mean"){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	606 #PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) t.test(x[condition_ind-1], x[control_ind-1])$p.value);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	607 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	608 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	609 if(method=="median"){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	610 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(wilcox.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	611 # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	612 }
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	613 }
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	614 PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	615
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	616
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	617 TE_colnames = colnames(TE_df_data);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	618 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	619 control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	620 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	621 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	622
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	623 if(method=="mean"){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	624 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) t.test(x[condition_ind-1], x[control_ind-1])$p.value);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	625 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	626 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	627 if(method=="median"){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	628 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(wilcox.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	629 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	630 }
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	631 }
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	632 TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	633
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	634
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	635 PE_TE_logfold_pval = data.frame(TE_df_logfold$Gene, TE_df_logfold$LogFold, TE_pval, TE_adj_pval, PE_df_logfold$LogFold, PE_pval, PE_adj_pval);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	636 colnames(PE_TE_logfold_pval) = c("Gene", "Transcript log fold-change", "p-value (transcript)", "adj p-value (transcript)", "Protein log fold-change", "p-value (protein)", "adj p-value (protein)");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	637 outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	638 write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	639 cat("<br><br><font size=5><b><a href='PE_TE_logfold_pval.txt' target='_blank'>Download the complete fold change data here</a></b></font><br>\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	640 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	641
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	642 if(length(condition_ind)!=1)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	643 {
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	644 # Volcano Plot
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	645
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	646 if(volc_with=="adj_pval")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	647 {
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	648 PE_pval = PE_adj_pval
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	649 TE_pval = TE_adj_pval
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	650 volc_ylab = "-log10 Adjusted p-value";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	651 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	652 if(volc_with=="pval")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	653 {
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	654 volc_ylab = "-log10 p-value";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	655 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	656 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	657 outplot_PE = paste(outdir,"/PE_volcano.png",sep="",collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	658 png(outplot_PE, width = 10, height = 10, units = 'in', res=300);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	659 # bitmap(outplot, "png16m");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	660 par(mfrow=c(1,1));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	661
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	662 plot(PE_df_logfold$LogFold, -log10(PE_pval),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	663 xlab="log2 fold change", ylab=volc_ylab,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	664 type="n")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	665 sel <- which((PE_df_logfold$LogFold<=log(2,base=2))&(PE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	666 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	667 PE_df_logfold$color <- "black"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	668 #sel <- which((PE_df_logfold$LogFold>log(2,base=2))&(PE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	669 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	670 sel1 <- which(PE_pval<=0.05)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	671 sel=intersect(sel,sel1)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	672 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	673 PE_df_logfold[sel,]$color <- "red"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	674 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	675 sel1 <- which(PE_pval>0.05)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	676 sel=intersect(sel,sel1)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	677 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	678 PE_df_logfold[sel,]$color <- "blue"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	679 abline(h = -log(0.05,base=10), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	680 abline(v = log(2,base=2), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	681 abline(v = log(0.5,base=2), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	682 dev.off();
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	683
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	684 g <- ggplot(PE_df_logfold, aes(x = LogFold, -log10(PE_pval), color = as.factor(color),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	685 text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	686 Genes, LogFold, -log10(PE_pval), PE_pval))) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	687 xlab("log2 fold change") + ylab("-log10 p-value") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	688 geom_point(shape=1, size = 1.5, stroke = .2) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	689 scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	690 geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	691 geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	692 geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	693 theme_light() + theme(legend.position="none")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	694 saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_PE)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	695
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	696 outplot_TE = paste(outdir,"/TE_volcano.png",sep="",collapse="");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	697 png(outplot_TE, width = 10, height = 10, units = 'in', res=300);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	698 # bitmap(outplot, "png16m");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	699 par(mfrow=c(1,1));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	700
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	701 plot(TE_df_logfold$LogFold, -log10(TE_pval),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	702 xlab="log2 fold change", ylab=volc_ylab,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	703 type="n")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	704
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	705 sel <- which((TE_df_logfold$LogFold<=log(2,base=2))&(TE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	706 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	707 TE_df_logfold$color <- "black"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	708 #sel <- which((TE_df_logfold$LogFold>log(2,base=2))&(TE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	709 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	710 sel1 <- which(TE_pval<=0.05)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	711 sel=intersect(sel,sel1)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	712 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	713 TE_df_logfold[sel,]$color <- "red"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	714 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	715 sel1 <- which(TE_pval>0.05)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	716 sel=intersect(sel,sel1)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	717 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	718 TE_df_logfold[sel,]$color <- "blue"
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	719 abline(h = -log(0.05,base=10), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	720 abline(v = log(2,base=2), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	721 abline(v = log(0.5,base=2), col="red", lty=2)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	722 dev.off();
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	723
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	724 g <- ggplot(TE_df_logfold, aes(x = LogFold, -log10(TE_pval), color = as.factor(color),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	725 text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	726 Genes, LogFold, -log10(TE_pval), TE_pval))) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	727 xlab("log2 fold change") + ylab("-log10 p-value") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	728 geom_point(shape=1, size = 1.5, stroke = .2) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	729 scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	730 geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	731 geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	732 geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") +
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	733 theme_light() + theme(legend.position="none")
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	734 saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_TE)))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	735
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	736
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	737 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Transcript Fold-Change</font></th><th><font color=#ffcc33>Protein Fold-Change</font></th></tr>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	738 cat("<tr><td align=center>",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	739 '<img src="TE_volcano.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	740 extractWidgetCode(outplot_TE)$widget_div,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	741 '</td>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	742 cat("<td align=center>",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	743 '<img src="PE_volcano.png" width=600 height=600>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	744 extractWidgetCode(outplot_PE)$widget_div,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	745 '</td></tr></table><br>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	746 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	747
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	748
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	749 }else{
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	750 cat('<br><br><b><font color=red>!!! No replicates found. Cannot perform test to check significance of differential expression. Thus, no Volcano plot generated !!!</font></b><br><br>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	751 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	752 }
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	753
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	754 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	755
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	756
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	757 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	758 # Functions: End
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	759 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	760
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	761
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	762 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	763 # Arguments
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	764 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	765 noargs = 12;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	766 args = commandArgs(trailingOnly = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	767 if(length(args) != noargs)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	768 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	769 stop(paste("Please check usage. Number of arguments is not equal to ",noargs,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	770 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	771
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	772 mode = args[1]; # "multiple" or "logfold"
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	773 method = args[2]; # "mean" or "median"
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	774 sampleinfo_file = args[3];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	775 proteome_file = args[4];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	776 transcriptome_file = args[5];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	777 correction_method = args[6];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	778 cookdist_upper_cutoff = args[7];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	779 numCluster = args[8];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	780 hm_nclust = args[9];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	781 volc_with = args[10];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	782
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	783 htmloutfile = args[11]; # html output file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	784 outdir = args[12]; # html supporting files
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	785
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	786 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	787 # Check for file existance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	788 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	789 if(! file.exists(proteome_file))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	790 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	791 stop(paste("Proteome Data file does not exists. Path given: ",proteome_file,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	792 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	793 if(! file.exists(transcriptome_file))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	794 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	795 stop(paste("Transcriptome Data file does not exists. Path given: ",transcriptome_file,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	796 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	797
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	798 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	799 # Load library
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	800 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	801 options(warn=-1);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	802
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	803 suppressPackageStartupMessages(library(dplyr));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	804 suppressPackageStartupMessages(library(data.table));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	805 suppressPackageStartupMessages(library(gplots));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	806 suppressPackageStartupMessages(library(ggplot2));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	807 suppressPackageStartupMessages(library(ggfortify));
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	808 suppressPackageStartupMessages(library(plotly));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	809 suppressPackageStartupMessages(library(d3heatmap));
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	810
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	811 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	812 # Select mode and parse experiment design file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	813 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	814 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	815 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	816 expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame();
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	817 expDesign_cc = expDesign[1:2,];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	818
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	819 sampleinfo_df = expDesign[3:nrow(expDesign),];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	820 rownames(sampleinfo_df)=1:nrow(sampleinfo_df);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	821 colnames(sampleinfo_df) = c("Sample","Group");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	822
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	823 condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	824 condition_g_name = "case";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	825 control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	826 control_g_name = "control";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	827 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	828 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control";
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	829 sampleinfo_df_orig = sampleinfo_df;
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	830 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	831
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	832 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	833 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	834 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	835 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	836
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	837 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	838 # Parse Transcriptome data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	839 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	840 TE_df_orig = fread(transcriptome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	841 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	842 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	843 TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)];
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	844 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	845 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	846 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	847 TE_df = TE_df_orig;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	848 colnames(TE_df) = c("Genes", "LogFold");
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	849 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	850 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	851 # Parse Proteome data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	852 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	853 PE_df_orig = fread(proteome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	854 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	855 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	856 PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)];
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	857 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	858 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	859 {
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	860 PE_df = PE_df_orig;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	861 colnames(PE_df) = c("Genes", "LogFold");
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	862 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	863
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	864 #=============================================================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	865 # Create directory structures and then set the working directory to output directory
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	866 #=============================================================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	867 if(! file.exists(outdir))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	868 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	869 dir.create(outdir);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	870 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	871 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	872 # Write initial data summary in html outfile
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	873 #===============================================================================
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	874 cat("<html><head></head><body>\n", file = htmloutfile);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	875
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	876 cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n",
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	877 "<font><h3>Input data summary</h3></font>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	878 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	879 "<li>Abbreviations used: PE (Proteome data) and TE (Transcriptome data)","</li><br>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	880 "<li>Input Proteome data dimension (Row Column): ", dim(PE_df)[1]," x ", dim(PE_df)[2],"</li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	881 "<li>Input Transcriptome data dimension (Row Column): ", dim(TE_df)[1]," x ", dim(TE_df)[2],"</li></ul><hr/>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	882 file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	883
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	884 cat("<h3 id=table_of_content>Table of Contents:</h3>\n",
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	885 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	886 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	887 "<li><a href=#corr_data>Correlation</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	888 "<li><a href=#regression_data>Regression analysis</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	889 "<li><a href=#inf_obs>Influential observations</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	890 "<li><a href=#cluster_data>Cluster analysis</a></li></ul><hr/>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	891 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	892 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	893 # Find common samples
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	894 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	895 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	896
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	897 if(length(common_samples)==0)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	898 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	899 stop("No common samples found ");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	900 cat("<b>Please check your experiment design file. Sample names (column names) in the Transcriptome and the Proteome data do not match. </b>\n",file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	901 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	902
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	903 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	904 # Create subsets based on common samples
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	905 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	906 TE_df = select(TE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	907 PE_df = select(PE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	908 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	909 rownames(sampleinfo_df) = sampleinfo_df[,1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	910
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	911 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	912 # Check for number of rows similarity
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	913 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	914 if(nrow(TE_df) != nrow(PE_df))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	915 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	916 stop("Number of rows in Transcriptome and Proteome data are not same i.e. they are not paired");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	917 cat("<b>The correlation analysis expects paired TE and PE data i.e. (i)th gene/transcript of TE file should correspond to (i)th protein of PE file. In the current input provided there is mismatch in terms of number of rows of TE and PE file. Please make sure you provide paired data.</b>\n",file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	918 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	919
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	920 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	921 # Number of groups
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	922 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	923 ngrps = unique(sampleinfo_df[,2]) %>% length();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	924 grps = unique(sampleinfo_df[,2]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	925 names(grps) = grps;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	926
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	927 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	928 # Change column1 name
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	929 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	930 colnames(TE_df)[1] = "Gene";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	931 colnames(PE_df)[1] = "Protein";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	932
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	933 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	934 # Treat missing values
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	935 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	936 TE_nacount = sum(is.na(TE_df));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	937 PE_nacount = sum(is.na(PE_df));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	938
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	939 TE_df[is.na(TE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	940 PE_df[is.na(PE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	941
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	942 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	943 # Obtain JS/HTML lines for interactive visualization
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	944 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	945 extractWidgetCode = function(outplot){
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	946 lines <- readLines(gsub("\\.png", "\\.html", outplot))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	947 return(list(
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	948 'prescripts' = c('',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	949 gsub('script', 'script',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	950 lines[grep('<head>',lines) + 3
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	951 :grep('</head>' ,lines) - 5]),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	952 ''),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	953 'widget_div' = paste('<!--',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	954 gsub('width:100%;height:400px',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	955 'width:500px;height:500px',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	956 lines[grep(lines, pattern='html-widget')]),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	957 '-->', sep=''),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	958 'postscripts' = paste('',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	959 gsub('script', 'script',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	960 lines[grep(lines, pattern='<script type')]),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	961 '', sep='')));
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	962 }
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	963 prescripts <- list()
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	964 postscripts <- list()
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	965
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	966
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	967 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	968 # Decide based on analysis mode
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	969 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	970 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	971 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	972 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	973 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	974
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	975 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	976 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	977 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	978 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	979 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	980 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	981
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	982 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	983 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	984 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	985 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	986
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	987 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	988 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	989
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	990 # TE PE scatter
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	991 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	992 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatter plot between Proteome and Transcriptome Abundance</font></th></tr>\n', file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	993 singlesample_scatter(PE_TE_data, outplot);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	994 lines <- extractWidgetCode(outplot);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	995 postscripts <- c(postscripts, lines$postscripts);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	996 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', lines$widget_div, '</td></tr>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	997 PE_TE_data = data.frame(PE_df, TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	998 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	999
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1000 # TE PE Cor
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1001 cat("<tr><td align=center>", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1002 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1003 cat('<font color="red">*Note that <u>correlation</u> is <u>sensitive to outliers</u> in the data. So it is important to analyze outliers/influential observations in the data.<br> Below we use <u>Cook\'s distance based approach</u> to identify such influential observations.</font>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1004 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1005 cat('</td></table>',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1006 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1007
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1008 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1009 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1010
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1011 # TE PE Regression
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1012 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1013 postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1014 extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1015 extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1016 extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1017 extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts));
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1018
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1019 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1020 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1021
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1022 # TE PE Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1023 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1024 lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse=""))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1025 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1026 prescripts <- c(prescripts, lines$prescripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1027
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1028
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1029 # TE PE Clustering (kmeans)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1030 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1031 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1032
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1033 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1034 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1035 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1036 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1037 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1038
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1039 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1040 outplot = paste(outdir,"/Box_TE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1041 temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)]));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1042 colnames(temp_df_te_data) = colnames(TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1043 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance (log)");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1044 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1045 prescripts <- c(prescripts, lines$prescripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1046 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1047 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1048 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1049 "<tr><td align=center>", file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1050 cat('<img src="Box_TE_all_rep.png" width=500 height=500>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1051 lines$widget_div, '</td>', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1052
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1053 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1054 outplot = paste(outdir,"/Box_PE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1055 temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)]));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1056 colnames(temp_df_pe_data) = colnames(PE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1057 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance (log)");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1058 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1059 #prescripts <- c(prescripts, lines$prescripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1060 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1061 cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500>',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1062 lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1063
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1064 # Calc TE PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1065 outplot = paste(outdir,"/PCA_TE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1066 multisample_PCA(TE_df, sampleinfo_df, outplot);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1067 PCA_TE <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1068 postscripts <- c(postscripts, PCA_TE$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1069
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1070 # Calc PE PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1071 outplot = paste(outdir,"/PCA_PE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1072 multisample_PCA(PE_df, sampleinfo_df, outplot);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1073 PCA_PE <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1074 postscripts <- c(postscripts, PCA_PE$postscripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1075
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1076 # Replicate mode
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1077 templist = mergeReplicates(TE_df,PE_df, sampleinfo_df, method);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1078 TE_df = templist$TE_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1079 PE_df = templist$PE_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1080 sampleinfo_df = templist$sampleinfo_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1081 rownames(sampleinfo_df) = sampleinfo_df[,1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1082
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1083 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1084 outplot = paste(outdir,"/Box_TE_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1085 temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)]));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1086 colnames(temp_df_te_data) = colnames(TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1087 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Transcript Abundance (log)");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1088 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1089 #prescripts <- c(prescripts, lines$prescripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1090 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1091 cat('<br><font color="#ff0000"><h3>Sample wise distribution (Box plot) after using ',method,' on replicates </h3></font><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1092 "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1093
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1094 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1095 outplot = paste(outdir,"/Box_PE_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1096 temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)]));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1097 colnames(temp_df_pe_data) = colnames(PE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1098 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Protein Abundance (log)");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1099 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1100 #prescripts <- c(prescripts, lines$prescripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1101 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1102 cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500>', lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1103
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1104 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1105 # Calculating log fold change and running the "single" code part
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1106 #===============================================================================
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1107
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1108 TE_df = data.frame("Genes"=TE_df[,1], "LogFold"=apply(TE_df[,c(which(colnames(TE_df)==condition_g_name),which(colnames(TE_df)==control_g_name))],1,function(x) log(x[1]/x[2],base=2)));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1109 PE_df = data.frame("Genes"=PE_df[,1], "LogFold"=apply(PE_df[,c(which(colnames(PE_df)==condition_g_name),which(colnames(PE_df)==control_g_name))],1,function(x) log(x[1]/x[2],base=2)));
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1110
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1111 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1112 # Treat missing values
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1113 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1114
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1115 TE_df[is.infinite(TE_df[,2]),2] = NA;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1116 PE_df[is.infinite(PE_df[,2]),2] = NA;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1117 TE_df[is.na(TE_df)] = 0;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1118 PE_df[is.na(PE_df)] = 0;
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1119
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1120 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1121 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1122 # Find common samples
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1123 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1124
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1125 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1126 TE_df = select(TE_df, 1, common_samples);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1127 PE_df = select(PE_df, 1, common_samples);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1128 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1129 rownames(sampleinfo_df) = sampleinfo_df[,1];
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1130
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1131 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1132 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1133 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)");
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1134 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1135 postscripts <- c(postscripts, lines$postscripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1136 cat('<br><font color="#ff0000"><h3>Distribution (Box plot) of log fold change </h3></font>', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1137 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1138 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1139
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1140 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1141 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1142 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Protein Abundance fold-change(log2)");
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1143 lines <- extractWidgetCode(outplot)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1144 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1145 cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500>', lines$widget_div,'</td></tr></table>\n', file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1146
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1147
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1148 # Log Fold Data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1149 perform_Test_Volcano(TE_df_orig,PE_df_orig,TE_df, PE_df,sampleinfo_df_orig,method,correction_method,volc_with)
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1150 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/TE_volcano.png",sep="",collapse=""))$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1151 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_volcano.png",sep="",collapse=""))$postscripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1152
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1153 # Print PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1154
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1155 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>PCA plot: Transcriptome data</font></th><th><font color=#ffcc33>PCA plot: Proteome data</font></th></tr>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1156 "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500>', PCA_TE$widget_div, '</td>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1157 "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500>', PCA_PE$widget_div, '</td></tr></table>\n',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1158 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1159
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1160
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1161
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1162 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1163 file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1164
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1165 PE_TE_data = data.frame(PE_df, TE_df);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1166 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1167
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1168 # TE PE scatter
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1169 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1170 cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Scatter plot between Proteome and Transcriptome Abundance</font></th></tr>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1171 singlesample_scatter(PE_TE_data, outplot);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1172 lines <- extractWidgetCode(outplot);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1173 postscripts <- c(postscripts, lines$postscripts);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1174 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', gsub('width:500px;height:500px', 'width:800px;height:800px' , lines$widget_div),
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1175 '</td>\n', file = htmloutfile, append = TRUE);
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1176
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1177 # TE PE Cor
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1178 cat("<tr><td align=center>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1179 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1180 cat('<font color="red">*Note that <u>correlation</u> is <u>sensitive to outliers</u> in the data. So it is important to analyze outliers/influential observations in the data.<br> Below we use <u>Cook\'s distance based approach</u> to identify such influential observations.</font>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1181 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1182 cat('</td></table>',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1183 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1184
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1185 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1186 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1187
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1188 # TE PE Regression
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1189 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1190 postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1191 extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1192 extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1193 extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1194 extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts,
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1195 gsub('data-for="html', 'data-for="secondhtml"',
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1196 extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$postscripts)));
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1197
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1198 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1199 file = htmloutfile, append = TRUE);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1200
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1201 #TE PE Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1202 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1203 lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse=""))
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1204 postscripts <- c(postscripts, lines$postscripts)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1205 prescripts <- c(prescripts, lines$prescripts)
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1206
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1207 #TE PE Clustering (kmeans)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1208 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1209 postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts);
0 75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1210 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1211 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1212 cat("<h3>Go To:</h3>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1213 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1214 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1215 "<li><a href=#corr_data>Correlation</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1216 "<li><a href=#regression_data>Regression analysis</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1217 "<li><a href=#inf_obs>Influential observations</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1218 "<li><a href=#cluster_data>Cluster analysis</a></li></ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1219 "<br><a href=#>TOP</a>",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1220 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1221 cat("</body></html>\n", file = htmloutfile, append = TRUE);
1 bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1222
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1223
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1224 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1225 # Add masked-javascripts tags to HTML file in the head and end
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1226 #===============================================================================
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1227
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1228 htmllines <- readLines(htmloutfile)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1229 htmllines[1] <- paste('<html>\n<head>\n', paste(prescripts, collapse='\n'), '\n</head>\n<body>')
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1230 cat(paste(htmllines, collapse='\n'), file = htmloutfile)
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1231 cat('\n', paste(postscripts, collapse='\n'), "\n",
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f galaxyp parents: 0 diff changeset	1232 "</body>\n</html>\n", file = htmloutfile, append = TRUE);

Mercurial > repos > galaxyp > quantp

annotate quantp.r @ 1:bcc7a4c4cc29 draft