quantp: quantp.r annotate

annotate quantp.r @ 0:75faf9a89f5b draft

planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6

author	galaxyp
date	Fri, 14 Sep 2018 12:22:31 -0400
parents
children	bcc7a4c4cc29

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$Group = tempgrp;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	16 png(outfile, width = 6, height = 6, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	17 # bitmap(outfile, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	18 g = autoplot(prcomp(select(tempdf, -Group)), data = tempdf, colour = 'Group', size=3);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	19 plot(g);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	20 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	21 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	22
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	23 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	24 # Regression and Cook's distance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	25 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	26 singlesample_regression = function(PE_TE_data,htmloutfile, append=TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	27 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	28 rownames(PE_TE_data) = PE_TE_data$PE_ID;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	29 regmodel = lm(PE_abundance~TE_abundance, data=PE_TE_data);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	30 regmodel_summary = summary(regmodel);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	31
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	32 cat("<font><h3>Linear Regression model fit between Proteome and Transcriptome data</h3></font>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	33 "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	34 '<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	35 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	36
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	37 cat("<tr><td>Formula</td><td>","PE_abundance~TE_abundance","</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	38 "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	39 "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	40 "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	41 "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	42 "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	43 "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	44 "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	45 "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	46 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	47
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	48 cat("</table>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	49
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	50 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	51 "<font color='#ff0000'><h3>Regression and diagnostics plots</h3></font>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	52 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	53
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	54 outplot = paste(outdir,"/PE_TE_lm_1.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	55 png(outplot, width = 10, height = 10, units = 'in',res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	56 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	57 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	58 plot(regmodel, 1, cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	59 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	60
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	61 outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	62 png(outplot,width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	63 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	64 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	65 plot(regmodel, 2, cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	66 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	67
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	68 outplot = paste(outdir,"/PE_TE_lm_5.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));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	72 plot(regmodel, 5, cex.lab=1.5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	73 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	74
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	75 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	76
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	77 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	78 '<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	79 '<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	80 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	81
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	82 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	83 '<tr><td align=center><img src="PE_TE_lm_1.png" width=600 height=600></td><td align=center><img src="PE_TE_lm_2.png" width=600 height=600></td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	84 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	85
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	86 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	87 '<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	88 '<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	89 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	90
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	91
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	92 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	93 # Residuals data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	94 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	95 res_all = regmodel$residuals;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	96 res_mean = mean(res_all);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	97 res_sd = sd(res_all);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	98 res_diff = (res_all-res_mean);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	99 res_zscore = res_diff/res_sd;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	100 # res_outliers = res_all[which((res_zscore > 2)\|(res_zscore < -2))]
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	101
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	102
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	103 tempind = which((res_zscore > 2)\|(res_zscore < -2));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	104 res_PE_TE_data_no_outlier = PE_TE_data[-tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	105 res_PE_TE_data_no_outlier$residuals = res_all[-tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	106 res_PE_TE_data_outlier = PE_TE_data[tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	107 res_PE_TE_data_outlier$residuals = res_all[tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	108
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	109 # Save the complete table for download (influential_observations)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	110 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)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	111 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	112 outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	113 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	114
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	115
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	116 # Save the complete table for download (non influential_observations)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	117 temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	118 colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	119 outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	120 write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	121
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	122
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	123 cat('<br><h2 id="inf_obs"><font color=#ff0000>Outliers based on the residuals from regression analysis</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	124 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	125 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	126 '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	127 '<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	128 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	129
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	130 cat("<tr><td>Mean Residual value</td><td>",res_mean,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	131 "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	132 '<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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	133 '<tr><td colspan=2 align=center><font size=4>(<b><a href=PE_TE_abundance_residuals.txt target="_blank">Download the complete residuals data here</a></b>)</font></td></td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	134 "</table><br><br>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	135 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	136
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	137 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	138
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	139
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	140 cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	141
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	142 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	143 '<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	144 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	145
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	146 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	147 '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600></td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	148 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	149
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	150 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	151 '<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	152 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	153
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	154
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	155
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	156 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	157 # Cook's Distance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	158 #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	159 cat('<hr/><h2 id="inf_obs"><font color=#ff0000>INFLUENTIAL OBSERVATIONS</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	160 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	161 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	162 '<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	163 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	164
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	165 cooksd <- cooks.distance(regmodel);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	166
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	167 outplot = paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	168 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	169 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	170 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	171 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	172 sel_outlier=which(cooksd>=as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	173 sel_nonoutlier=which(cooksd<as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	174 points(sel_outlier, cooksd[sel_outlier],pch="*", cex=2, cex.lab=1.5, col="red")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	175 points(sel_nonoutlier, cooksd[sel_nonoutlier],pch="*", cex=2, cex.lab=1.5, col="black")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	176 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	177 #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	178 dev.off();
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 '<img src="PE_TE_lm_cooksd.png" width=800 height=800>',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	182 '<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	183 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	184
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	185 tempind = which(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	186 PE_TE_data_no_outlier = PE_TE_data[-tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	187 PE_TE_data_no_outlier$cooksd = cooksd[-tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	188 PE_TE_data_outlier = PE_TE_data[tempind,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	189 PE_TE_data_outlier$cooksd = cooksd[tempind];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	190 a = sort(PE_TE_data_outlier$cooksd, decreasing=T, index.return=T);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	191 PE_TE_data_outlier_sorted = PE_TE_data_outlier[a$ix,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	192
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	193 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	194 '<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	195 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	196
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	197 # Save the complete table for download (influential_observations)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	198 temp_outlier_data = data.frame(PE_TE_data_outlier$PE_ID, PE_TE_data_outlier$TE_abundance, PE_TE_data_outlier$PE_abundance, PE_TE_data_outlier$cooksd)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	199 colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	200 outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	201 write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	202
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	203
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	204 # Save the complete table for download (non influential_observations)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	205 temp_no_outlier_data = data.frame(PE_TE_data_no_outlier$PE_ID, PE_TE_data_no_outlier$TE_abundance, PE_TE_data_no_outlier$PE_abundance, PE_TE_data_no_outlier$cooksd)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	206 colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	207 outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	208 write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	209
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	210
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	211 cat("<tr><td>Mean Cook\'s distance</td><td>",mean(cooksd, na.rm=T),"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	212 "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	213
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	214 "<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",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	215 "</table><br><br>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	216 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	217
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	218
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	219 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	220 # Scatter plot after removal of influential points
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	221 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	222 outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	223 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	224 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	225 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	226 # bitmap(outplot,"png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	227 g = ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance))+geom_point() + geom_smooth() + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + xlim(min_lim,max_lim) + ylim(min_lim,max_lim);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	228 suppressMessages(plot(g));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	229 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	230
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	231 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);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	232 # Before
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	233 cat("<tr><td align=center><!--<font color='#ff0000'><h3>Scatter plot between Proteome and Transcriptome Abundance</h3></font>\n-->", '<img src="TE_PE_scatter.png" width=600 height=600></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	234
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	235 # After
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	236 cat("<td align=center>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	237 '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600></td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	238 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	239 #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	240
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	241
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	242 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	243 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	244 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	245
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	246 cat('<tr><td>\n', file = htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	247 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	248 cat('</td>\n', file = htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	249
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	250
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	251 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	252 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	253
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	254 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	255 "<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	256 "<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	257 file = htmloutfile, append = TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	258 cat("</table></td></tr></table>\n", file = htmloutfile, append = TRUE)
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
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	262 if(dim(PE_TE_data_outlier)[1]<10)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	263 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	264 tab_n_row = dim(PE_TE_data_outlier)[1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	265 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	266 tab_n_row = 10;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	267 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	268
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	269 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>    ",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	270 "<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",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	271 '<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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	272 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	273
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	274 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	275 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",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	276 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	277
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	278
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	279 for(i in 1:tab_n_row)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	280 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	281 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	282 '<tr>','<td>',as.character(PE_TE_data_outlier_sorted[i,1]),'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	283 '<td>',format(PE_TE_data_outlier_sorted[i,2], scientific=F),'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	284 '<td>',PE_TE_data_outlier_sorted[i,4],'</td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	285 '<td>',format(PE_TE_data_outlier_sorted[i,5], scientific=F),'</td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	286 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	287 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	288 cat('</table><br><br>\n',file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	289
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	290
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	291 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	292
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	293
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	294
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	295 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	296 # Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	297 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	298 singlesample_heatmap=function(PE_TE_data, htmloutfile, hm_nclust){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	299 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	300 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	301
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	302 hc=hclust(dist(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")])))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	303 hm_cluster = cutree(hc,k=hm_nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	304
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	305 outplot = paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	306 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	307 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	308 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	309 hmap = heatmap.2(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]), trace="none", cexCol=1, col=greenred(100),Colv=F, labCol=c("Proteins","Transcripts"), scale="col", hclustfun = hclust, distfun = dist);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	310 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	311
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	312 cat('<tr><td align=center colspan="2"><img src="PE_TE_heatmap.png" width=800 height=800></td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	313 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	314
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	315
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	316 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	317 colnames(temp_PE_TE_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cluster (Hierarchical clustering)")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	318 tempoutfile = paste(outdir,"/PE_TE_hc_clusterpoints.txt",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	319 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	320
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	321
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	322 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	323 file = htmloutfile, append = TRUE);
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
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	327 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	328 # K-means clustering
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	329 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	330 singlesample_kmeans=function(PE_TE_data, htmloutfile, nclust){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	331 PE_TE_data_kdata = PE_TE_data;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	332 k1 = kmeans(PE_TE_data_kdata[,c("PE_abundance","TE_abundance")], nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	333 outplot = paste(outdir,"/PE_TE_kmeans.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	334 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	335 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	336 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	337 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	338 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	339 legend(1, 95, legend="Cluster 2", col="green", lty=1:1, cex=0.8)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	340
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	341
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	342 ind=which(k1$cluster==1);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	343 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="red", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	344 ind=which(k1$cluster==2);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	345 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	346 ind=which(k1$cluster==3);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	347 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="blue", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	348 ind=which(k1$cluster==4);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	349 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	350 ind=which(k1$cluster==5);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	351 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="black", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	352 ind=which(k1$cluster==6);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	353 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	354 ind=which(k1$cluster==7);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	355 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="gold", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	356 ind=which(k1$cluster==8);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	357 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	358 ind=which(k1$cluster==9);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	359 points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="yellow", pch=16);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	360 ind=which(k1$cluster==10);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	361 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	362 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	363
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	364 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	365 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	366
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	367 tempind = order(k1$cluster);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	368 tempoutfile = paste(outdir,"/PE_TE_kmeans_clusterpoints.txt",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	369 write.table(data.frame(PE_TE_data_kdata[tempind, ], Cluster=k1$cluster[tempind]), file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	370
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	371
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	372 cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800></td></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	373 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	374 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	375 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	376
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	377 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	378
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	379 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	380 # scatter plot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	381 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	382 singlesample_scatter = function(PE_TE_data, outfile)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	383 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	384 min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	385 max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	386 png(outfile, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	387 # bitmap(outfile, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	388 g = ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance))+geom_point() + geom_smooth() + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + xlim(min_lim,max_lim) + ylim(min_lim,max_lim);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	389 suppressMessages(plot(g));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	390 # plot(g);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	391 dev.off();
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 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	395 # Correlation table
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	396 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	397 singlesample_cor = function(PE_TE_data, htmloutfile, append=TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	398 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	399 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	400 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	401 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	402
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	403 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	404 '<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	405 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	406
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	407 cat(
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	408 "<tr><td>Correlation method</td><td>",cor_result_pearson$method,"</td><td>",cor_result_spearman$method,"</td><td>",cor_result_kendall$method,"</td></tr>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	409 "<tr><td>Correlation coefficient</td><td>",cor_result_pearson$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	410 file = htmloutfile, append = TRUE)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	411 cat("</table>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	412
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	413 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	414
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	415 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	416 # Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	417 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	418 multisample_boxplot = function(df, sampleinfo_df, outfile, fill_leg, user_xlab, user_ylab)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	419 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	420 tempdf = df[,-1, drop=FALSE];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	421 tempdf = t(tempdf) %>% as.data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	422 tempdf[is.na(tempdf)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	423 tempdf$Sample = rownames(tempdf);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	424 tempdf1 = melt(tempdf, id.vars = "Sample");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	425 tempdf1$Group = sampleinfo_df[tempdf1$Sample,2];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	426 png(outplot, width = 6, height = 6, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	427 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	428 if(fill_leg=="Yes")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	429 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	430 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	431 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	432 if(fill_leg=="No")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	433 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	434 tempdf1$Group = c("case", "control")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	435 g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	436 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	437 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	438 plot(g);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	439 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	440 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	441
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	442
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	443 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	444 # Mean or Median of Replicates
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	445 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	446
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	447 mergeReplicates = function(TE_df,PE_df, sampleinfo_df, method)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	448 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	449 grps = unique(sampleinfo_df[,2]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	450
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	451 TE_df_merged <<- sapply(grps, function(x){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	452 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	453 if(length(tempsample)!=1){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	454 apply(TE_df[,tempsample],1,method);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	455 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	456 return(TE_df[,tempsample]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	457 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	458 });
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	459 TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	460 colnames(TE_df_merged) = c(colnames(TE_df)[1], grps);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	461
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	462 PE_df_merged <<- sapply(grps, function(x){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	463 tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1]
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	464 if(length(tempsample)!=1){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	465 apply(PE_df[,tempsample],1,method);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	466 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	467 return(PE_df[,tempsample]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	468 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	469 });
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	470
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	471 PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	472 colnames(PE_df_merged) = c(colnames(PE_df)[1], grps);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	473
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	474 #sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	475 sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	476
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	477 return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	478 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	479
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	480 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	481 # (T-Test or Wilcoxon ranksum test) and Volcano Plot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	482 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	483
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	484 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	485 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	486
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	487 PE_colnames = colnames(PE_df_data);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	488 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	489 control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	490 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	491 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)});
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	492
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	493 if(method=="mean"){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	494 #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])$p.value);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	495 PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	496 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	497 if(method=="median"){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	498 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$p.value)}})
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	499 # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	500 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	501 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	502 PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	503
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	504
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	505 TE_colnames = colnames(TE_df_data);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	506 control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	507 control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	508 condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	509 condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)});
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	510
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	511 if(method=="mean"){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	512 # 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])$p.value);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	513 TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}})
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	514 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	515 if(method=="median"){
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	516 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$p.value)}})
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	517 # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	518 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	519 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	520 TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	521
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	522
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	523 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);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	524 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)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	525 outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	526 write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	527 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",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	528 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	529
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	530 if(length(condition_ind)!=1)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	531 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	532 # Volcano Plot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	533
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	534 if(volc_with=="adj_pval")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	535 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	536 PE_pval = PE_adj_pval
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	537 TE_pval = TE_adj_pval
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	538 volc_ylab = "-log10 Adjusted p-value";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	539 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	540 if(volc_with=="pval")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	541 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	542 volc_ylab = "-log10 p-value";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	543 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	544 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	545 outplot = paste(outdir,"/PE_volcano.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	546 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	547 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	548 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	549
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	550 plot(PE_df_logfold$LogFold, -log10(PE_pval),
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	551 xlab="log2 fold change", ylab=volc_ylab,
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	552 type="n")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	553 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
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	554 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	555 #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
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	556 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	557 sel1 <- which(PE_pval<=0.05)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	558 sel=intersect(sel,sel1)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	559 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	560 sel <- which((PE_df_logfold$LogFold>log(2,base=2))\|(PE_df_logfold$LogFold<log(0.5, base=2)))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	561 sel1 <- which(PE_pval>0.05)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	562 sel=intersect(sel,sel1)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	563 points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	564 abline(h = -log(0.05,base=10), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	565 abline(v = log(2,base=2), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	566 abline(v = log(0.5,base=2), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	567 dev.off();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	568
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	569
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	570
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	571 outplot = paste(outdir,"/TE_volcano.png",sep="",collapse="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	572 png(outplot, width = 10, height = 10, units = 'in', res=300);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	573 # bitmap(outplot, "png16m");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	574 par(mfrow=c(1,1));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	575
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	576 plot(TE_df_logfold$LogFold, -log10(TE_pval),
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	577 xlab="log2 fold change", ylab=volc_ylab,
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	578 type="n")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	579 sel <- which((TE_df_logfold$LogFold<=log(2,base=2))&(TE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	580 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	581 #sel <- which((TE_df_logfold$LogFold>log(2,base=2))&(TE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	582 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	583 sel1 <- which(TE_pval<=0.05)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	584 sel=intersect(sel,sel1)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	585 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	586 sel <- which((TE_df_logfold$LogFold>log(2,base=2))\|(TE_df_logfold$LogFold<log(0.5, base=2)))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	587 sel1 <- which(TE_pval>0.05)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	588 sel=intersect(sel,sel1)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	589 points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	590 abline(h = -log(0.05,base=10), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	591 abline(v = log(2,base=2), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	592 abline(v = log(0.5,base=2), col="red", lty=2)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	593 dev.off();
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
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	597 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);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	598 cat("<tr><td align=center>", '<img src="TE_volcano.png" width=600 height=600></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	599 cat("<td align=center>",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	600 '<img src="PE_volcano.png" width=600 height=600></td></tr></table><br>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	601 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	602 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	603 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>',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	604 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	605 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	606
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	607 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	608
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	609
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	610 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	611 # Functions: End
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	612 #***************************************************************************************************************************************
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	613
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	614
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	615
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	616
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	617 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	618 # Arguments
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	619 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	620 noargs = 12;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	621 args = commandArgs(trailingOnly = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	622 if(length(args) != noargs)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	623 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	624 stop(paste("Please check usage. Number of arguments is not equal to ",noargs,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	625 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	626
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	627 mode = args[1]; # "multiple" or "logfold"
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	628 method = args[2]; # "mean" or "median"
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	629 sampleinfo_file = args[3];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	630 proteome_file = args[4];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	631 transcriptome_file = args[5];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	632 correction_method = args[6];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	633 cookdist_upper_cutoff = args[7];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	634 numCluster = args[8];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	635 hm_nclust = args[9];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	636 volc_with = args[10];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	637
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	638 htmloutfile = args[11]; # html output file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	639 outdir = args[12]; # html supporting files
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	640
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	641
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	642 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	643 # Check for file existance
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	644 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	645 if(! file.exists(proteome_file))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	646 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	647 stop(paste("Proteome Data file does not exists. Path given: ",proteome_file,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	648 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	649 if(! file.exists(transcriptome_file))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	650 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	651 stop(paste("Transcriptome Data file does not exists. Path given: ",transcriptome_file,sep="",collapse=""));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	652 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	653
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	654 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	655 # Load library
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	656 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	657 options(warn=-1);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	658
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	659 suppressPackageStartupMessages(library(dplyr));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	660 suppressPackageStartupMessages(library(data.table));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	661 suppressPackageStartupMessages(library(gplots));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	662 suppressPackageStartupMessages(library(ggplot2));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	663 suppressPackageStartupMessages(library(ggfortify));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	664
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	665 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	666 # Select mode and parse experiment design file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	667 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	668 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	669 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	670 expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	671 expDesign_cc = expDesign[1:2,];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	672
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	673 sampleinfo_df = expDesign[3:nrow(expDesign),];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	674 rownames(sampleinfo_df)=1:nrow(sampleinfo_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	675 colnames(sampleinfo_df) = c("Sample","Group");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	676
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	677 condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	678 condition_g_name = "case";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	679 control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	680 control_g_name = "control";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	681 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	682 sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	683 sampleinfo_df_orig = sampleinfo_df;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	684 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	685
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	686 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	687 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	688 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	689 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	690
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	691 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	692 # Parse Transcriptome data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	693 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	694 TE_df_orig = fread(transcriptome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	695 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	696 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	697 TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	698 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	699 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	700 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	701 TE_df = TE_df_orig;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	702 colnames(TE_df) = c("Genes", "LogFold");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	703 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	704 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	705 # Parse Proteome data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	706 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	707 PE_df_orig = fread(proteome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	708 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	709 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	710 PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	711 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	712 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	713 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	714 PE_df = PE_df_orig;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	715 colnames(PE_df) = c("Genes", "LogFold");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	716 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	717
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	718 #=============================================================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	719 # Create directory structures and then set the working directory to output directory
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	720 #=============================================================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	721 if(! file.exists(outdir))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	722 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	723 dir.create(outdir);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	724 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	725 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	726 # Write initial data summary in html outfile
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	727 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	728 cat("<html><head></head><body>\n", file = htmloutfile);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	729
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	730 cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	731 "<font><h3>Input data summary</h3></font>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	732 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	733 "<li>Abbreviations used: PE (Proteome data) and TE (Transcriptome data)","</li><br>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	734 "<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	735 "<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	736 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	737
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	738 cat("<h3 id=table_of_content>Table of Contents:</h3>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	739 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	740 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	741 "<li><a href=#corr_data>Correlation</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	742 "<li><a href=#regression_data>Regression analysis</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	743 "<li><a href=#inf_obs>Influential observations</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	744 "<li><a href=#cluster_data>Cluster analysis</a></li></ul><hr/>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	745 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	746 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	747 # Find common samples
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	748 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	749 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	750
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	751 if(length(common_samples)==0)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	752 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	753 stop("No common samples found ");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	754 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	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 # Create subsets based on common samples
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	759 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	760 TE_df = select(TE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	761 PE_df = select(PE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	762 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	763 rownames(sampleinfo_df) = sampleinfo_df[,1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	764
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	765 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	766 # Check for number of rows similarity
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	767 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	768 if(nrow(TE_df) != nrow(PE_df))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	769 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	770 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	771 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	772 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	773
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	774 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	775 # Number of groups
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	776 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	777 ngrps = unique(sampleinfo_df[,2]) %>% length();
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	778 grps = unique(sampleinfo_df[,2]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	779 names(grps) = grps;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	780
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	781 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	782 # Change column1 name
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	783 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	784 colnames(TE_df)[1] = "Gene";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	785 colnames(PE_df)[1] = "Protein";
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	786
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	787 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	788 # Treat missing values
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	789 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	790 TE_nacount = sum(is.na(TE_df));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	791 PE_nacount = sum(is.na(PE_df));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	792
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	793 TE_df[is.na(TE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	794 PE_df[is.na(PE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	795
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 # Decide based on analysis mode
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	799 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	800 if(mode=="logfold")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	801 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	802 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	803 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	804
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	805 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	806 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	807 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	808 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	809 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	810 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	811
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	812 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	813 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	814 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	815 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	816
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	817 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	818 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	819
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	820 # TE PE scatter
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	821 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	822 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);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	823 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td></tr>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	824 PE_TE_data = data.frame(PE_df, TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	825 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	826 singlesample_scatter(PE_TE_data, outplot);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	827
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	828 # TE PE Cor
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	829 cat("<tr><td align=center>", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	830 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	831 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	832 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	833 cat('</td></table>',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	834 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	835
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	836 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	837 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	838
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	839 # TE PE Regression
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	840 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	841
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	842 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	843 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	844
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	845 # TE PE Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	846 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	847
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	848
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	849 # TE PE Clustering (kmeans)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	850 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	851
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	852 }else{
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	853 if(mode=="multiple")
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	854 {
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	855 cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	856 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	857
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	858 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	859 outplot = paste(outdir,"/Box_TE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	860 cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	861 '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	862 "<tr><td align=center>", '<img src="Box_TE_all_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	863 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	864 colnames(temp_df_te_data) = colnames(TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	865 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance (log)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	866
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	867 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	868 outplot = paste(outdir,"/Box_PE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	869 cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	870 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	871 colnames(temp_df_pe_data) = colnames(PE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	872 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance (log)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	873
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	874 # Calc TE PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	875 outplot = paste(outdir,"/PCA_TE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	876 multisample_PCA(TE_df, sampleinfo_df, outplot);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	877
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	878 # Calc PE PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	879 outplot = paste(outdir,"/PCA_PE_all_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	880 multisample_PCA(PE_df, sampleinfo_df, outplot);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	881
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	882
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	883 # Replicate mode
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	884 templist = mergeReplicates(TE_df,PE_df, sampleinfo_df, method);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	885 TE_df = templist$TE_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	886 PE_df = templist$PE_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	887 sampleinfo_df = templist$sampleinfo_df_merged;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	888 rownames(sampleinfo_df) = sampleinfo_df[,1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	889
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	890 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	891 outplot = paste(outdir,"/Box_TE_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	892 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	893 "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	894 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	895 colnames(temp_df_te_data) = colnames(TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	896 multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Transcript Abundance (log)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	897
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	898 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	899 outplot = paste(outdir,"/Box_PE_rep.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	900 cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	901 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	902 colnames(temp_df_pe_data) = colnames(PE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	903 multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Protein Abundance (log)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	904
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	905 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	906 # Calculating log fold change and running the "single" code part
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	907 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	908
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	909 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	910 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)));
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	911
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	912 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	913 # Treat missing values
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	914 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	915
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	916 TE_df[is.infinite(TE_df[,2]),2] = NA;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	917 PE_df[is.infinite(PE_df[,2]),2] = NA;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	918 TE_df[is.na(TE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	919 PE_df[is.na(PE_df)] = 0;
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	920
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	921 sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change"))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	922 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	923 # Find common samples
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	924 #===============================================================================
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	925
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	926 common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	927 TE_df = select(TE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	928 PE_df = select(PE_df, 1, common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	929 sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	930 rownames(sampleinfo_df) = sampleinfo_df[,1];
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	931
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	932 # TE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	933 outplot = paste(outdir,"/Box_TE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	934 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	935 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	936 "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	937 multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	938
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	939 # PE Boxplot
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	940 outplot = paste(outdir,"/Box_PE.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	941 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	942 multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Protein Abundance fold-change(log2)");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	943
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	944
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	945 # Log Fold Data
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	946 perform_Test_Volcano(TE_df_orig,PE_df_orig,TE_df, PE_df,sampleinfo_df_orig,method,correction_method,volc_with)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	947
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	948
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	949
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	950 # Print PCA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	951
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	952 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	953 "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500></td>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	954 "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500></td></tr></table>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	955 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	956
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	957
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	958
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	959 cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	960 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	961
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	962 # TE PE scatter
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	963 outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape="");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	964 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	965 cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td>\n', file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	966 PE_TE_data = data.frame(PE_df, TE_df);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	967 colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance");
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	968 singlesample_scatter(PE_TE_data, outplot);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	969
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	970 # TE PE Cor
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	971 cat("<tr><td align=center>\n", file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	972 singlesample_cor(PE_TE_data, htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	973 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',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	974 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	975 cat('</td></table>',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	976 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	977
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	978 cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	979 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	980
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	981 # TE PE Regression
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	982 singlesample_regression(PE_TE_data,htmloutfile, append=TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	983
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	984 cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n',
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	985 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	986
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	987 #TE PE Heatmap
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	988 singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	989
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	990 #TE PE Clustering (kmeans)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	991 singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster))
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	992
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	993 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	994 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	995 cat("<h3>Go To:</h3>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	996 "<ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	997 "<li><a href=#sample_dist>Sample distribution</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	998 "<li><a href=#corr_data>Correlation</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	999 "<li><a href=#regression_data>Regression analysis</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1000 "<li><a href=#inf_obs>Influential observations</a></li>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1001 "<li><a href=#cluster_data>Cluster analysis</a></li></ul>\n",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1002 "<br><a href=#>TOP</a>",
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1003 file = htmloutfile, append = TRUE);
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6 galaxyp parents: diff changeset	1004 cat("</body></html>\n", file = htmloutfile, append = TRUE);

Mercurial > repos > galaxyp > quantp

annotate quantp.r @ 0:75faf9a89f5b draft