Mercurial > repos > galaxyp > quantp
changeset 1:bcc7a4c4cc29 draft
planemo upload commit 1887dff812162880d66b003a927867cd5000c98f
| author | galaxyp |
|---|---|
| date | Thu, 20 Dec 2018 16:06:05 -0500 |
| parents | 75faf9a89f5b |
| children | ed0bb50d7ffe |
| files | quantp.r quantp.xml |
| diffstat | 2 files changed, 596 insertions(+), 365 deletions(-) [+] |
line wrap: on
line diff
--- a/quantp.r Fri Sep 14 12:22:31 2018 -0400 +++ b/quantp.r Thu Dec 20 16:06:05 2018 -0500 @@ -16,6 +16,7 @@ png(outfile, width = 6, height = 6, units = 'in', res=300); # bitmap(outfile, "png16m"); g = autoplot(prcomp(select(tempdf, -Group)), data = tempdf, colour = 'Group', size=3); + saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outplot))) plot(g); dev.off(); } @@ -30,20 +31,20 @@ regmodel_summary = summary(regmodel); cat("<font><h3>Linear Regression model fit between Proteome and Transcriptome data</h3></font>\n", - "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n", - '<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', - file = htmloutfile, append = TRUE); + "<p>Assuming a linear relationship between Proteome and Transcriptome data, we here fit a linear regression model.</p>\n", + '<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', + file = htmloutfile, append = TRUE); cat("<tr><td>Formula</td><td>","PE_abundance~TE_abundance","</td></tr>\n", - "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n", - "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n", - "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n", - "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n", - "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n", - "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n", - "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n", - "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n", - file = htmloutfile, append = TRUE); + "<tr><td colspan='2' align='center'> <b>Coefficients</b></td>","</tr>\n", + "<tr><td>",names(regmodel$coefficients[1]),"</td><td>",regmodel$coefficients[1]," (Pvalue:", regmodel_summary$coefficients[1,4],")","</td></tr>\n", + "<tr><td>",names(regmodel$coefficients[2]),"</td><td>",regmodel$coefficients[2]," (Pvalue:", regmodel_summary$coefficients[2,4],")","</td></tr>\n", + "<tr><td colspan='2' align='center'> <b>Model parameters</b></td>","</tr>\n", + "<tr><td>Residual standard error</td><td>",regmodel_summary$sigma," (",regmodel_summary$df[2]," degree of freedom)</td></tr>\n", + "<tr><td>F-statistic</td><td>",regmodel_summary$fstatistic[1]," ( on ",regmodel_summary$fstatistic[2]," and ",regmodel_summary$fstatistic[3]," degree of freedom)</td></tr>\n", + "<tr><td>R-squared</td><td>",regmodel_summary$r.squared,"</td></tr>\n", + "<tr><td>Adjusted R-squared</td><td>",regmodel_summary$adj.r.squared,"</td></tr>\n", + file = htmloutfile, append = TRUE); cat("</table>\n", file = htmloutfile, append = TRUE); @@ -58,13 +59,27 @@ plot(regmodel, 1, cex.lab=1.5); dev.off(); + suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[1]] + + geom_point(aes(text=sprintf("Residual: %.2f<br>Fitted value: %.2f<br>Gene: %s", .fitted, .resid, PE_TE_data$PE_ID)), + shape = 1, size = .1, stroke = .2) + + theme_light()) + saveWidget(ggplotly(g, tooltip= c("text")), file.path(gsub("\\.png", "\\.html", outplot))) + outplot = paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""); png(outplot,width = 10, height = 10, units = 'in', res=300); # bitmap(outplot, "png16m"); par(mfrow=c(1,1)); - plot(regmodel, 2, cex.lab=1.5); + g <- plot(regmodel, 2, cex.lab=1.5); + ggplotly(g) dev.off(); + suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[2]] + + geom_point(aes(text=sprintf("Standarized residual: %.2f<br>Theoretical quantile: %.2f<br>Gene: %s", .qqx, .qqy, PE_TE_data$PE_ID)), + shape = 1, size = .1) + + theme_light()) + saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot))) + + outplot = paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""); png(outplot, width = 10, height = 10, units = 'in',res=300); # bitmap(outplot, "png16m"); @@ -72,79 +87,94 @@ plot(regmodel, 5, cex.lab=1.5); dev.off(); + cd_cont_pos <- function(leverage, level, model) {sqrt(level*length(coef(model))*(1-leverage)/leverage)} + cd_cont_neg <- function(leverage, level, model) {-cd_cont_pos(leverage, level, model)} + + suppressWarnings(g <- autoplot(regmodel, label = FALSE)[[4]] + + aes(label = PE_TE_data$PE_ID) + + geom_point(aes(text=sprintf("Leverage: %.2f<br>Standardized residual: %.2f<br>Gene: %s", .hat, .stdresid, PE_TE_data$PE_ID))) + + theme_light()) + saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outplot))) + cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE); - cat( + cat( '<tr bgcolor="#7a0019"><th>', "<font color='#ffcc33'><h4>1) <u>Residuals vs Fitted plot</h4></font></u></th>\n", '<th><font color=#ffcc33><h4>2) <u>Normal Q-Q plot of residuals</h4></font></u></th></tr>\n', file = htmloutfile, append = TRUE); cat( - '<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', - file = htmloutfile, append = TRUE); + '<tr><td align=center><img src="PE_TE_lm_1.png" width=600 height=600>', + gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$widget_div), + '</td><td align=center><img src="PE_TE_lm_2.png" width=600 height=600>', + gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$widget_div), + '</td></tr>\n', file = htmloutfile, append = TRUE); cat( '<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', '<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', file = htmloutfile, append = TRUE); - - - #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - # Residuals data - #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - res_all = regmodel$residuals; - res_mean = mean(res_all); - res_sd = sd(res_all); - res_diff = (res_all-res_mean); - res_zscore = res_diff/res_sd; - # res_outliers = res_all[which((res_zscore > 2)|(res_zscore < -2))] - - - tempind = which((res_zscore > 2)|(res_zscore < -2)); - res_PE_TE_data_no_outlier = PE_TE_data[-tempind,]; - res_PE_TE_data_no_outlier$residuals = res_all[-tempind]; - res_PE_TE_data_outlier = PE_TE_data[tempind,]; - res_PE_TE_data_outlier$residuals = res_all[tempind]; + + + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ + # Residuals data + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ + res_all = regmodel$residuals; + res_mean = mean(res_all); + res_sd = sd(res_all); + res_diff = (res_all-res_mean); + res_zscore = res_diff/res_sd; + # res_outliers = res_all[which((res_zscore > 2)|(res_zscore < -2))] + + + tempind = which((res_zscore > 2)|(res_zscore < -2)); + res_PE_TE_data_no_outlier = PE_TE_data[-tempind,]; + res_PE_TE_data_no_outlier$residuals = res_all[-tempind]; + res_PE_TE_data_outlier = PE_TE_data[tempind,]; + res_PE_TE_data_outlier$residuals = res_all[tempind]; # Save the complete table for download (influential_observations) - 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) - colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value") - outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse=""); - write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); + 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) + colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value") + outdatafile = paste(outdir,"/PE_TE_outliers_residuals.txt", sep="", collapse=""); + write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); # Save the complete table for download (non influential_observations) - temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all) - colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value") - outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse=""); - write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F); + temp_all_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, res_all) + colnames(temp_all_data) = c("Gene", "Transcript abundance", "Protein abundance", "Residual value") + outdatafile = paste(outdir,"/PE_TE_abundance_residuals.txt", sep="", collapse=""); + write.table(temp_all_data, file=outdatafile, row.names=F, sep="\t", quote=F); cat('<br><h2 id="inf_obs"><font color=#ff0000>Outliers based on the residuals from regression analysis</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n', - '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n', - '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n', - file = htmloutfile, append = TRUE); - + '<tr bgcolor="#7a0019"><th colspan=2><font color=#ffcc33>Residuals from Regression</font></th></tr>\n', + '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Parameter</font></th><th><font color=#ffcc33>Value</font></th></tr>\n', + file = htmloutfile, append = TRUE); + cat("<tr><td>Mean Residual value</td><td>",res_mean,"</td></tr>\n", - "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n", - '<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', - '<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', - "</table><br><br>\n", - file = htmloutfile, append = TRUE); - + "<tr><td>Standard deviation (Residuals)</td><td>",res_sd,"</td></tr>\n", + '<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', + '<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></tr>\n</table><br><br>\n", + file = htmloutfile, append = TRUE); + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - - + + cat('<br><br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">', file = htmloutfile, append = TRUE); - + cat( '<tr bgcolor="#7a0019"><th><font color=#ffcc33><h4>3) <u>Residuals vs Leverage plot</h4></font></u></th></tr>\n', file = htmloutfile, append = TRUE); cat( - '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600></td></tr>\n', + '<tr><td align=center><img src="PE_TE_lm_5.png" width=600 height=600>', + gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$widget_div) + , '</td></tr>\n', file = htmloutfile, append = TRUE); cat( @@ -157,7 +187,7 @@ # Cook's Distance #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ cat('<hr/><h2 id="inf_obs"><font color=#ff0000>INFLUENTIAL OBSERVATIONS</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat( '<p><b>Cook\'s distance</b> computes the influence of each data point/observation on the predicted outcome. i.e. this measures how much the observation is influencing the fitted values.<br>In general use, those observations that have a <b>Cook\'s distance > than ', cookdist_upper_cutoff,' times the mean</b> may be classified as <b>influential.</b></p>\n', file = htmloutfile, append = TRUE); @@ -177,11 +207,31 @@ #text(x=1:length(cooksd)+1, y=cooksd, labels=ifelse(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T),names(cooksd),""), col="red", pos=2) # add labels dev.off(); + cooksd_df <- data.frame(cooksd) + cooksd_df$genes <- row.names(cooksd_df) + cooksd_df$index <- 1:nrow(cooksd_df) + cooksd_df$colors <- "black" + cutoff <- as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T) + cooksd_df[cooksd_df$cooksd > cutoff,]$colors <- "red" + + g <- ggplot(cooksd_df, aes(x = index, y = cooksd, label = row.names(cooksd_df), color=as.factor(colors), + text=sprintf("Gene: %s<br>Cook's Distance: %.3f", row.names(cooksd_df), cooksd))) + + ggtitle("Influential Obs. by Cook's distance") + xlab("Observations") + ylab("Cook's Distance") + + #xlim(0, 3000) + ylim(0, .15) + + scale_shape_discrete(solid=F) + + geom_point(size = 2, shape = 8) + + geom_hline(yintercept = cutoff, + linetype = "dashed", color = "red") + + scale_color_manual(values = c("black" = "black", "red" = "red")) + + theme_light() + theme(legend.position="none") + saveWidget(ggplotly(g, tooltip= "text"), file.path(gsub("\\.png", "\\.html", outplot))) + cat( '<img src="PE_TE_lm_cooksd.png" width=800 height=800>', + gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div), '<br>In the above plot, observations above red line (',cookdist_upper_cutoff,' * mean Cook\'s distance) are influential. Genes that are outliers could be important. These observations influences the correlation values and regression coefficients<br><br>', file = htmloutfile, append = TRUE); - + tempind = which(cooksd>as.numeric(cookdist_upper_cutoff)*mean(cooksd, na.rm=T)); PE_TE_data_no_outlier = PE_TE_data[-tempind,]; PE_TE_data_no_outlier$cooksd = cooksd[-tempind]; @@ -195,49 +245,63 @@ file = htmloutfile, append = TRUE); # Save the complete table for download (influential_observations) - 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) - colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance") - outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse=""); - write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); + 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) + colnames(temp_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance") + outdatafile = paste(outdir,"/PE_TE_influential_observation.txt", sep="", collapse=""); + write.table(temp_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); # Save the complete table for download (non influential_observations) - 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) - colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance") - outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse=""); - write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); + 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) + colnames(temp_no_outlier_data) = c("Gene", "Transcript abundance", "Protein abundance", "Cook's distance") + outdatafile = paste(outdir,"/PE_TE_non_influential_observation.txt", sep="", collapse=""); + write.table(temp_no_outlier_data, file=outdatafile, row.names=F, sep="\t", quote=F); cat("<tr><td>Mean Cook\'s distance</td><td>",mean(cooksd, na.rm=T),"</td></tr>\n", - "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n", - - "<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", - "</table><br><br>\n", - file = htmloutfile, append = TRUE); - - - #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - # Scatter plot after removal of influential points - #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""); - min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance)); - max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance)); - png(outplot, width = 10, height = 10, units = 'in', res=300); - # bitmap(outplot,"png16m"); - 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); - suppressMessages(plot(g)); - dev.off(); - - 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); - # Before - 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); - - # After - cat("<td align=center>\n", - '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600></td></tr>\n', - file = htmloutfile, append = TRUE); - #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - + "<tr><td>Total influential observations (Cook\'s distance > ",cookdist_upper_cutoff," * mean Cook\'s distance)</td><td>",length(tempind),"</td>\n", + + "<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", + "</table><br><br>\n", + file = htmloutfile, append = TRUE); + + + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ + # Scatter plot after removal of influential points + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ + outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""); + min_lim = min(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance)); + max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance)); + png(outplot, width = 10, height = 10, units = 'in', res=300); + # bitmap(outplot,"png16m"); + suppressWarnings(g <- ggplot(PE_TE_data_no_outlier, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() + + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + + xlim(min_lim,max_lim) + ylim(min_lim,max_lim) + + geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f", + PE_ID, TE_abundance, PE_abundance)))) + suppressMessages(plot(g)) + suppressMessages(saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot)))) + dev.off(); + + + 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); + # Before + 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>', + gsub('id="html', 'id="secondhtml"', + gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$widget_div)), + '</td>\n', + file = htmloutfile, append = TRUE); + + # After + cat("<td align=center>\n", + '<img src="AbundancePlot_scatter_without_outliers.png" width=600 height=600>', + gsub("width:500px;height:500px", "width:600px;height:600px", extractWidgetCode(outplot)$widget_div), + + '</td></tr>\n', + file = htmloutfile, append = TRUE); + #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ + cor_result_pearson = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "pearson"); cor_result_spearman = cor.test(PE_TE_data_no_outlier[,"TE_abundance"], PE_TE_data_no_outlier[,"PE_abundance"], method = "spearman"); @@ -249,7 +313,7 @@ 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', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat( "<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", @@ -267,13 +331,13 @@ } 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> ", - "<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", - '<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', - file = htmloutfile, append = TRUE); + "<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", + '<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', + file = htmloutfile, append = TRUE); cat('<table border=1 cellspacing=0 cellpadding=5> <tr bgcolor="#7a0019">\n', sep = "",file = htmloutfile, append = TRUE); 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", - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); for(i in 1:tab_n_row) @@ -285,9 +349,9 @@ '<td>',format(PE_TE_data_outlier_sorted[i,5], scientific=F),'</td></tr>\n', file = htmloutfile, append = TRUE); } - cat('</table><br><br>\n',file = htmloutfile, append = TRUE); - - + cat('</table><br><br>\n',file = htmloutfile, append = TRUE); + + } @@ -297,7 +361,7 @@ #=============================================================================== singlesample_heatmap=function(PE_TE_data, htmloutfile, hm_nclust){ 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', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); hc=hclust(dist(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]))) hm_cluster = cutree(hc,k=hm_nclust); @@ -306,11 +370,25 @@ png(outplot, width = 10, height = 10, units = 'in', res=300); # bitmap(outplot, "png16m"); par(mfrow=c(1,1)); - 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); + 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); + dev.off(); - cat('<tr><td align=center colspan="2"><img src="PE_TE_heatmap.png" width=800 height=800></td></tr>\n', - file = htmloutfile, append = TRUE); + + p <- d3heatmap(as.matrix(PE_TE_data[,c("PE_abundance","TE_abundance")]), scale = "col", + dendrogram = "row", colors = greenred(100), + hclustfun = hclust, distfun = dist, + show_grid = FALSE) + saveWidget(p, file.path(gsub("\\.png", "\\.html", outplot))) + + cat('<tr><td align=center colspan="2">', + '<img src="PE_TE_heatmap.png" width=800 height=800>', + gsub("width:960px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div), + '</td></tr>\n', + file = htmloutfile, append = TRUE); temp_PE_TE_data = data.frame(PE_TE_data$PE_ID, PE_TE_data$TE_abundance, PE_TE_data$PE_abundance, hm_cluster); @@ -320,7 +398,7 @@ cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_hc_clusterpoints.txt" target="_blank"><b>Download the hierarchical cluster list</b></a></font></td></tr></table>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); } @@ -338,7 +416,6 @@ legend(1, 95, legend=c("Cluster 1", "Line 2"), col="red", lty=1:1, cex=0.8) legend(1, 95, legend="Cluster 2", col="green", lty=1:1, cex=0.8) - ind=which(k1$cluster==1); points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="red", pch=16); ind=which(k1$cluster==2); @@ -361,18 +438,30 @@ points(PE_TE_data_kdata[ind,"TE_abundance"], PE_TE_data_kdata[ind,"PE_abundance"], col="orange", pch=16); dev.off(); + # Interactive plot for k-means clustering + g <- ggplot(PE_TE_data, aes(x = TE_abundance, y = PE_abundance, label = row.names(PE_TE_data), + text=sprintf("Gene: %s<br>Transcript Abundance: %.3f<br>Protein Abundance: %.3f", + PE_ID, TE_abundance, PE_abundance), + color=as.factor(k1$cluster))) + + xlab("Transcript Abundance") + ylab("Protein Abundance") + + scale_shape_discrete(solid=F) + geom_smooth(method = "loess", span = 2/3) + + geom_point(size = 1, shape = 8) + + theme_light() + theme(legend.position="none") + saveWidget(ggplotly(g, tooltip=c("text")), file.path(gsub("\\.png", "\\.html", outplot))) + 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', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); tempind = order(k1$cluster); tempoutfile = paste(outdir,"/PE_TE_kmeans_clusterpoints.txt",sep="",collapse=""); write.table(data.frame(PE_TE_data_kdata[tempind, ], Cluster=k1$cluster[tempind]), file=tempoutfile, row.names=F, quote=F, sep="\t", eol="\n") - - cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800></td></tr>\n', - file = htmloutfile, append = TRUE); + #paste(outdir,"/PE_TE_heatmap.png",sep="",collapse=""); + cat('<tr><td colspan="2" align=center><img src="PE_TE_kmeans.png" width=800 height=800>', + gsub("width:500px;height:500px", "width:800px;height:800px", extractWidgetCode(outplot)$widget_div), '</td></tr>\n', + file = htmloutfile, append = TRUE); cat('<tr><td colspan="2" align=center><font size=5><a href="PE_TE_kmeans_clusterpoints.txt" target="_blank"><b>Download the cluster list</b></a></font></td></tr></table><br><hr/>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); } @@ -385,9 +474,14 @@ max_lim = max(c(PE_TE_data$PE_abundance,PE_TE_data$TE_abundance)); png(outfile, width = 10, height = 10, units = 'in', res=300); # bitmap(outfile, "png16m"); - g = ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance))+geom_point() + geom_smooth() + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + xlim(min_lim,max_lim) + ylim(min_lim,max_lim); - suppressMessages(plot(g)); - # plot(g); + suppressWarnings(g <- ggplot(PE_TE_data, aes(x=TE_abundance, y=PE_abundance, label=PE_ID)) + geom_smooth() + + xlab("Transcript abundance log fold-change") + ylab("Protein abundance log fold-change") + + xlim(min_lim,max_lim) + ylim(min_lim,max_lim) + + geom_point(aes(text=sprintf("Gene: %s<br>Transcript Abundance (log fold-change): %.3f<br>Protein Abundance (log fold-change): %.3f", + PE_ID, TE_abundance, PE_abundance)), + size = .5)) + suppressMessages(plot(g)) + suppressMessages(saveWidget(ggplotly(g, tooltip = "text"), file.path(gsub("\\.png", "\\.html", outfile)))) dev.off(); } @@ -422,23 +516,41 @@ tempdf[is.na(tempdf)] = 0; tempdf$Sample = rownames(tempdf); tempdf1 = melt(tempdf, id.vars = "Sample"); + + if("Gene" %in% colnames(df)){ + tempdf1$Name = df$Gene; + } else if ("Protein" %in% colnames(df)){ + tempdf1$Name = df$Protein; + } else if ("Genes" %in% colnames(df)){ + tempdf1$Name = df$Genes; + } + tempdf1$Group = sampleinfo_df[tempdf1$Sample,2]; png(outplot, width = 6, height = 6, units = 'in', res=300); # bitmap(outplot, "png16m"); - if(fill_leg=="Yes") - { - g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab) - }else{ - if(fill_leg=="No") - { - tempdf1$Group = c("case", "control") - g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + geom_boxplot() + labs(x=user_xlab) + labs(y=user_ylab) - } + if(fill_leg=="No"){ + tempdf1$Group = c("case", "control") } + + g = ggplot(tempdf1, aes(x=Sample, y=value, fill=Group)) + + geom_boxplot()+ + labs(x=user_xlab) + labs(y=user_ylab) + saveWidget(ggplotly(g), file.path(gsub("\\.png", "\\.html", outfile))) plot(g); dev.off(); } +## A wrapper to saveWidget which compensates for arguable BUG in +## saveWidget which requires `file` to be in current working +## directory. +saveWidget <- function (widget,file,...) { + wd<-getwd() + on.exit(setwd(wd)) + outDir<-dirname(file) + file<-basename(file) + setwd(outDir); + htmlwidgets::saveWidget(widget,file=file,selfcontained = FALSE) +} #=============================================================================== # Mean or Median of Replicates @@ -446,35 +558,35 @@ mergeReplicates = function(TE_df,PE_df, sampleinfo_df, method) { -grps = unique(sampleinfo_df[,2]); - -TE_df_merged <<- sapply(grps, function(x){ - tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1] - if(length(tempsample)!=1){ - apply(TE_df[,tempsample],1,method); - }else{ - return(TE_df[,tempsample]); - } -}); -TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged); -colnames(TE_df_merged) = c(colnames(TE_df)[1], grps); - -PE_df_merged <<- sapply(grps, function(x){ - tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1] - if(length(tempsample)!=1){ - apply(PE_df[,tempsample],1,method); - }else{ - return(PE_df[,tempsample]); - } -}); - -PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged); -colnames(PE_df_merged) = c(colnames(PE_df)[1], grps); - -#sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F); -sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F); - -return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged)); + grps = unique(sampleinfo_df[,2]); + + TE_df_merged <<- sapply(grps, function(x){ + tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1] + if(length(tempsample)!=1){ + apply(TE_df[,tempsample],1,method); + }else{ + return(TE_df[,tempsample]); + } + }); + TE_df_merged <<- data.frame(as.character(TE_df[,1]), TE_df_merged); + colnames(TE_df_merged) = c(colnames(TE_df)[1], grps); + + PE_df_merged <<- sapply(grps, function(x){ + tempsample = sampleinfo_df[which(sampleinfo_df$Group==x),1] + if(length(tempsample)!=1){ + apply(PE_df[,tempsample],1,method); + }else{ + return(PE_df[,tempsample]); + } + }); + + PE_df_merged <<- data.frame(as.character(PE_df[,1]), PE_df_merged); + colnames(PE_df_merged) = c(colnames(PE_df)[1], grps); + + #sampleinfo_df_merged = data.frame(Sample = grps, Group = grps, stringsAsFactors = F); + sampleinfo_df_merged = data.frame(Sample = grps, Group = "Group", stringsAsFactors = F); + + return(list(TE_df_merged = TE_df_merged, PE_df_merged = PE_df_merged, sampleinfo_df_merged = sampleinfo_df_merged)); } #=============================================================================== @@ -483,127 +595,162 @@ perform_Test_Volcano = function(TE_df_data,PE_df_data,TE_df_logfold, PE_df_logfold,sampleinfo_df, method, correction_method,volc_with) { - -PE_colnames = colnames(PE_df_data); -control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1]; -control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)}); -condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1]; -condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)}); - -if(method=="mean"){ - #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])$p.value); - PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}}) -}else{ -if(method=="median"){ - 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$p.value)}}) - # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value); + + PE_colnames = colnames(PE_df_data); + control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1]; + control_ind <<- sapply(control_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)}); + condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1]; + condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(PE_colnames==x); as.numeric(temp_ind)}); + + if(method=="mean"){ + #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])$p.value); + PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}}) + }else{ + if(method=="median"){ + 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$p.value)}}) + # PE_pval = apply(PE_df_data[2:length(colnames(PE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value); + } } -} -PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval)) - - -TE_colnames = colnames(TE_df_data); -control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1]; -control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)}); -condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1]; -condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)}); - -if(method=="mean"){ - # 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])$p.value); - TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}}) -}else{ - if(method=="median"){ - 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$p.value)}}) - # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value); + PE_adj_pval = p.adjust(PE_pval, method = correction_method, n = length(PE_pval)) + + + TE_colnames = colnames(TE_df_data); + control_sample = sampleinfo_df[which(sampleinfo_df$Group=="control"),1]; + control_ind <<- sapply(control_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)}); + condition_sample = sampleinfo_df[which(sampleinfo_df$Group=="case"),1]; + condition_ind <<- sapply(condition_sample, function(x){temp_ind = which(TE_colnames==x); as.numeric(temp_ind)}); + + if(method=="mean"){ + # 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])$p.value); + TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) {obj<-try(t.test(x[condition_ind-1], x[control_ind-1]),silent=TRUE); if(is(obj, "try-error")){return(NA)}else{return(obj$p.value)}}) + }else{ + if(method=="median"){ + 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$p.value)}}) + # TE_pval = apply(TE_df_data[2:length(colnames(TE_df_data))],1,function(x) wilcox.test(x[condition_ind-1], x[control_ind-1])$p.value); + } } -} -TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval)) - - -PE_TE_logfold_pval = data.frame(TE_df_logfold$Gene, TE_df_logfold$LogFold, TE_pval, TE_adj_pval, PE_df_logfold$LogFold, PE_pval, PE_adj_pval); -colnames(PE_TE_logfold_pval) = c("Gene", "Transcript log fold-change", "p-value (transcript)", "adj p-value (transcript)", "Protein log fold-change", "p-value (protein)", "adj p-value (protein)"); -outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse=""); -write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F); -cat("<br><br><font size=5><b><a href='PE_TE_logfold_pval.txt' target='_blank'>Download the complete fold change data here</a></b></font><br>\n", - file = htmloutfile, append = TRUE); - - if(length(condition_ind)!=1) - { - # Volcano Plot - - if(volc_with=="adj_pval") - { - PE_pval = PE_adj_pval - TE_pval = TE_adj_pval - volc_ylab = "-log10 Adjusted p-value"; - }else{ - if(volc_with=="pval") - { - volc_ylab = "-log10 p-value"; - } - } - outplot = paste(outdir,"/PE_volcano.png",sep="",collapse=""); - png(outplot, width = 10, height = 10, units = 'in', res=300); - # bitmap(outplot, "png16m"); - par(mfrow=c(1,1)); + TE_adj_pval = p.adjust(TE_pval, method = correction_method, n = length(TE_pval)) + + + PE_TE_logfold_pval = data.frame(TE_df_logfold$Gene, TE_df_logfold$LogFold, TE_pval, TE_adj_pval, PE_df_logfold$LogFold, PE_pval, PE_adj_pval); + 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)"); + outdatafile = paste(outdir,"/PE_TE_logfold_pval.txt", sep="", collapse=""); + write.table(PE_TE_logfold_pval, file=outdatafile, row.names=F, sep="\t", quote=F); + 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", + file = htmloutfile, append = TRUE); - plot(PE_df_logfold$LogFold, -log10(PE_pval), - xlab="log2 fold change", ylab=volc_ylab, - type="n") - sel <- which((PE_df_logfold$LogFold<=log(2,base=2))&(PE_df_logfold$LogFold>=log(0.5, base=2))) # or whatever you want to use - points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black") - #sel <- which((PE_df_logfold$LogFold>log(2,base=2))&(PE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use - sel <- which((PE_df_logfold$LogFold>log(2,base=2))|(PE_df_logfold$LogFold<log(0.5, base=2))) - sel1 <- which(PE_pval<=0.05) - sel=intersect(sel,sel1) - points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red") - sel <- which((PE_df_logfold$LogFold>log(2,base=2))|(PE_df_logfold$LogFold<log(0.5, base=2))) - sel1 <- which(PE_pval>0.05) - sel=intersect(sel,sel1) - points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue") - abline(h = -log(0.05,base=10), col="red", lty=2) - abline(v = log(2,base=2), col="red", lty=2) - abline(v = log(0.5,base=2), col="red", lty=2) - dev.off(); + if(length(condition_ind)!=1) + { + # Volcano Plot + + if(volc_with=="adj_pval") + { + PE_pval = PE_adj_pval + TE_pval = TE_adj_pval + volc_ylab = "-log10 Adjusted p-value"; + }else{ + if(volc_with=="pval") + { + volc_ylab = "-log10 p-value"; + } + } + outplot_PE = paste(outdir,"/PE_volcano.png",sep="",collapse=""); + png(outplot_PE, width = 10, height = 10, units = 'in', res=300); + # bitmap(outplot, "png16m"); + par(mfrow=c(1,1)); + + plot(PE_df_logfold$LogFold, -log10(PE_pval), + xlab="log2 fold change", ylab=volc_ylab, + type="n") + 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 + points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="black") + PE_df_logfold$color <- "black" + #sel <- which((PE_df_logfold$LogFold>log(2,base=2))&(PE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use + sel <- which((PE_df_logfold$LogFold>log(2,base=2))|(PE_df_logfold$LogFold<log(0.5, base=2))) + sel1 <- which(PE_pval<=0.05) + sel=intersect(sel,sel1) + points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="red") + PE_df_logfold[sel,]$color <- "red" + sel <- which((PE_df_logfold$LogFold>log(2,base=2))|(PE_df_logfold$LogFold<log(0.5, base=2))) + sel1 <- which(PE_pval>0.05) + sel=intersect(sel,sel1) + points(PE_df_logfold[sel,"LogFold"], -log10(PE_pval[sel]),col="blue") + PE_df_logfold[sel,]$color <- "blue" + abline(h = -log(0.05,base=10), col="red", lty=2) + abline(v = log(2,base=2), col="red", lty=2) + abline(v = log(0.5,base=2), col="red", lty=2) + dev.off(); + + g <- ggplot(PE_df_logfold, aes(x = LogFold, -log10(PE_pval), color = as.factor(color), + text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f", + Genes, LogFold, -log10(PE_pval), PE_pval))) + + xlab("log2 fold change") + ylab("-log10 p-value") + + geom_point(shape=1, size = 1.5, stroke = .2) + + scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) + + geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") + + geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") + + geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") + + theme_light() + theme(legend.position="none") + saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_PE))) + + outplot_TE = paste(outdir,"/TE_volcano.png",sep="",collapse=""); + png(outplot_TE, width = 10, height = 10, units = 'in', res=300); + # bitmap(outplot, "png16m"); + par(mfrow=c(1,1)); + + plot(TE_df_logfold$LogFold, -log10(TE_pval), + xlab="log2 fold change", ylab=volc_ylab, + type="n") + + 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 + points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black") + TE_df_logfold$color <- "black" + #sel <- which((TE_df_logfold$LogFold>log(2,base=2))&(TE_df_logfold$LogFold<log(0.5,base=2))) # or whatever you want to use + sel <- which((TE_df_logfold$LogFold>log(2,base=2))|(TE_df_logfold$LogFold<log(0.5, base=2))) + sel1 <- which(TE_pval<=0.05) + sel=intersect(sel,sel1) + points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red") + TE_df_logfold[sel,]$color <- "red" + sel <- which((TE_df_logfold$LogFold>log(2,base=2))|(TE_df_logfold$LogFold<log(0.5, base=2))) + sel1 <- which(TE_pval>0.05) + sel=intersect(sel,sel1) + points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue") + TE_df_logfold[sel,]$color <- "blue" + abline(h = -log(0.05,base=10), col="red", lty=2) + abline(v = log(2,base=2), col="red", lty=2) + abline(v = log(0.5,base=2), col="red", lty=2) + dev.off(); + + g <- ggplot(TE_df_logfold, aes(x = LogFold, -log10(TE_pval), color = as.factor(color), + text=sprintf("Gene: %s<br>Log2 Fold-Change: %.3f<br>-log10 p-value: %.3f<br>p-value: %.3f", + Genes, LogFold, -log10(TE_pval), TE_pval))) + + xlab("log2 fold change") + ylab("-log10 p-value") + + geom_point(shape=1, size = 1.5, stroke = .2) + + scale_color_manual(values = c("black" = "black", "red" = "red", "blue" = "blue")) + + geom_hline(yintercept = -log(0.05,base=10), linetype="dashed", color="red") + + geom_vline(xintercept = log(2,base=2), linetype="dashed", color="red") + + geom_vline(xintercept = log(0.5,base=2), linetype="dashed", color="red") + + theme_light() + theme(legend.position="none") + saveWidget(ggplotly(g, tooltip="text"), file.path(gsub("\\.png", "\\.html", outplot_TE))) + + + cat('<br><table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Transcript Fold-Change</font></th><th><font color=#ffcc33>Protein Fold-Change</font></th></tr>\n', file = htmloutfile, append = TRUE); + cat("<tr><td align=center>", + '<img src="TE_volcano.png" width=600 height=600>', + extractWidgetCode(outplot_TE)$widget_div, + '</td>\n', file = htmloutfile, append = TRUE); + cat("<td align=center>", + '<img src="PE_volcano.png" width=600 height=600>', + extractWidgetCode(outplot_PE)$widget_div, + '</td></tr></table><br>\n', + file = htmloutfile, append = TRUE); + + + }else{ + cat('<br><br><b><font color=red>!!! No replicates found. Cannot perform test to check significance of differential expression. Thus, no Volcano plot generated !!!</font></b><br><br>', + file = htmloutfile, append = TRUE); + } - - - outplot = paste(outdir,"/TE_volcano.png",sep="",collapse=""); - png(outplot, width = 10, height = 10, units = 'in', res=300); - # bitmap(outplot, "png16m"); - par(mfrow=c(1,1)); - - plot(TE_df_logfold$LogFold, -log10(TE_pval), - xlab="log2 fold change", ylab=volc_ylab, - type="n") - 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 - points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="black") - #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 - sel <- which((TE_df_logfold$LogFold>log(2,base=2))|(TE_df_logfold$LogFold<log(0.5, base=2))) - sel1 <- which(TE_pval<=0.05) - sel=intersect(sel,sel1) - points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="red") - sel <- which((TE_df_logfold$LogFold>log(2,base=2))|(TE_df_logfold$LogFold<log(0.5, base=2))) - sel1 <- which(TE_pval>0.05) - sel=intersect(sel,sel1) - points(TE_df_logfold[sel,"LogFold"], -log10(TE_pval[sel]),col="blue") - abline(h = -log(0.05,base=10), col="red", lty=2) - abline(v = log(2,base=2), col="red", lty=2) - abline(v = log(0.5,base=2), col="red", lty=2) - dev.off(); - - - - 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); - cat("<tr><td align=center>", '<img src="TE_volcano.png" width=600 height=600></td>\n', file = htmloutfile, append = TRUE); - cat("<td align=center>", - '<img src="PE_volcano.png" width=600 height=600></td></tr></table><br>\n', - file = htmloutfile, append = TRUE); - }else{ - 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>', - file = htmloutfile, append = TRUE); - } - } @@ -612,8 +759,6 @@ #*************************************************************************************************************************************** - - #=============================================================================== # Arguments #=============================================================================== @@ -638,7 +783,6 @@ htmloutfile = args[11]; # html output file outdir = args[12]; # html supporting files - #=============================================================================== # Check for file existance #=============================================================================== @@ -661,31 +805,33 @@ suppressPackageStartupMessages(library(gplots)); suppressPackageStartupMessages(library(ggplot2)); suppressPackageStartupMessages(library(ggfortify)); +suppressPackageStartupMessages(library(plotly)); +suppressPackageStartupMessages(library(d3heatmap)); #=============================================================================== # Select mode and parse experiment design file #=============================================================================== if(mode=="multiple") { - expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame(); - expDesign_cc = expDesign[1:2,]; - - sampleinfo_df = expDesign[3:nrow(expDesign),]; - rownames(sampleinfo_df)=1:nrow(sampleinfo_df); - colnames(sampleinfo_df) = c("Sample","Group"); - - condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1]; - condition_g_name = "case"; - control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1]; - control_g_name = "control"; - sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case"; - sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control"; - sampleinfo_df_orig = sampleinfo_df; + expDesign = fread(sampleinfo_file, header = FALSE, stringsAsFactors = FALSE, sep="\t") %>% data.frame(); + expDesign_cc = expDesign[1:2,]; + + sampleinfo_df = expDesign[3:nrow(expDesign),]; + rownames(sampleinfo_df)=1:nrow(sampleinfo_df); + colnames(sampleinfo_df) = c("Sample","Group"); + + condition_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),1]; + condition_g_name = "case"; + control_cols = sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),1]; + control_g_name = "control"; + sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="case"),2]),2] = "case"; + sampleinfo_df[which(sampleinfo_df[,2]==expDesign_cc[which(expDesign_cc[,1]=="control"),2]),2] = "control"; + sampleinfo_df_orig = sampleinfo_df; } if(mode=="logfold") { - sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change")) + sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change")) } #=============================================================================== @@ -694,12 +840,12 @@ TE_df_orig = fread(transcriptome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame(); if(mode=="multiple") { - TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)]; + TE_df = TE_df_orig[,c(colnames(TE_df_orig)[1],condition_cols,control_cols)]; } if(mode=="logfold") { - TE_df = TE_df_orig; - colnames(TE_df) = c("Genes", "LogFold"); + TE_df = TE_df_orig; + colnames(TE_df) = c("Genes", "LogFold"); } #=============================================================================== # Parse Proteome data @@ -707,12 +853,12 @@ PE_df_orig = fread(proteome_file, sep="\t", stringsAsFactor=F, header=T) %>% data.frame(); if(mode=="multiple") { - PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)]; + PE_df = PE_df_orig[,c(colnames(PE_df_orig)[1],condition_cols,control_cols)]; } if(mode=="logfold") { - PE_df = PE_df_orig; - colnames(PE_df) = c("Genes", "LogFold"); + PE_df = PE_df_orig; + colnames(PE_df) = c("Genes", "LogFold"); } #============================================================================================================= @@ -725,17 +871,17 @@ #=============================================================================== # Write initial data summary in html outfile #=============================================================================== - cat("<html><head></head><body>\n", file = htmloutfile); - - cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n", +cat("<html><head></head><body>\n", file = htmloutfile); + +cat("<h1><u>QuanTP: Association between abundance ratios of transcript and protein</u></h1><hr/>\n", "<font><h3>Input data summary</h3></font>\n", "<ul>\n", "<li>Abbreviations used: PE (Proteome data) and TE (Transcriptome data)","</li><br>\n", "<li>Input Proteome data dimension (Row Column): ", dim(PE_df)[1]," x ", dim(PE_df)[2],"</li>\n", "<li>Input Transcriptome data dimension (Row Column): ", dim(TE_df)[1]," x ", dim(TE_df)[2],"</li></ul><hr/>\n", file = htmloutfile, append = TRUE); - - cat("<h3 id=table_of_content>Table of Contents:</h3>\n", + +cat("<h3 id=table_of_content>Table of Contents:</h3>\n", "<ul>\n", "<li><a href=#sample_dist>Sample distribution</a></li>\n", "<li><a href=#corr_data>Correlation</a></li>\n", @@ -793,6 +939,30 @@ TE_df[is.na(TE_df)] = 0; PE_df[is.na(PE_df)] = 0; +#=============================================================================== +# Obtain JS/HTML lines for interactive visualization +#=============================================================================== +extractWidgetCode = function(outplot){ + lines <- readLines(gsub("\\.png", "\\.html", outplot)) + return(list( + 'prescripts' = c('', + gsub('script', 'script', + lines[grep('<head>',lines) + 3 + :grep('</head>' ,lines) - 5]), + ''), + 'widget_div' = paste('<!--', + gsub('width:100%;height:400px', + 'width:500px;height:500px', + lines[grep(lines, pattern='html-widget')]), + '-->', sep=''), + 'postscripts' = paste('', + gsub('script', 'script', + lines[grep(lines, pattern='<script type')]), + '', sep=''))); +} +prescripts <- list() +postscripts <- list() + #=============================================================================== # Decide based on analysis mode @@ -800,13 +970,13 @@ if(mode=="logfold") { cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE Boxplot outplot = paste(outdir,"/Box_TE.png",sep="",collape=""); cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n', - '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n', - "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE); + '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n', + "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE); multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance data"); # PE Boxplot @@ -815,70 +985,93 @@ multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance data"); cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE PE scatter outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape=""); 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); - cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td></tr>\n', file = htmloutfile, append = TRUE); + singlesample_scatter(PE_TE_data, outplot); + lines <- extractWidgetCode(outplot); + postscripts <- c(postscripts, lines$postscripts); + cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', lines$widget_div, '</td></tr>\n', file = htmloutfile, append = TRUE); PE_TE_data = data.frame(PE_df, TE_df); colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance"); - singlesample_scatter(PE_TE_data, outplot); # TE PE Cor cat("<tr><td align=center>", file = htmloutfile, append = TRUE); singlesample_cor(PE_TE_data, htmloutfile, append=TRUE); 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', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat('</td></table>', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE PE Regression singlesample_regression(PE_TE_data,htmloutfile, append=TRUE); + postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts)); cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE PE Heatmap singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust); + lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="")) + postscripts <- c(postscripts, lines$postscripts) + prescripts <- c(prescripts, lines$prescripts) # TE PE Clustering (kmeans) singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster)) + postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts) }else{ if(mode=="multiple") { cat('<h2 id="sample_dist"><font color=#ff0000>SAMPLE DISTRIBUTION</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE Boxplot outplot = paste(outdir,"/Box_TE_all_rep.png",sep="",collape=""); - cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n', - '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n', - "<tr><td align=center>", '<img src="Box_TE_all_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE); temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)])); colnames(temp_df_te_data) = colnames(TE_df); multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "Yes", "Samples", "Transcript Abundance (log)"); + lines <- extractWidgetCode(outplot) + prescripts <- c(prescripts, lines$prescripts) + postscripts <- c(postscripts, lines$postscripts) + cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; ">\n', + '<tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n', + "<tr><td align=center>", file = htmloutfile, append = TRUE); + cat('<img src="Box_TE_all_rep.png" width=500 height=500>', + lines$widget_div, '</td>', file = htmloutfile, append = TRUE); # PE Boxplot outplot = paste(outdir,"/Box_PE_all_rep.png",sep="",collape=""); - cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE); temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)])); colnames(temp_df_pe_data) = colnames(PE_df); multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "Yes", "Samples", "Protein Abundance (log)"); + lines <- extractWidgetCode(outplot) + #prescripts <- c(prescripts, lines$prescripts) + postscripts <- c(postscripts, lines$postscripts) + cat("<td align=center>", '<img src="Box_PE_all_rep.png" width=500 height=500>', + lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE); # Calc TE PCA outplot = paste(outdir,"/PCA_TE_all_rep.png",sep="",collape=""); multisample_PCA(TE_df, sampleinfo_df, outplot); - + PCA_TE <- extractWidgetCode(outplot) + postscripts <- c(postscripts, PCA_TE$postscripts) + # Calc PE PCA outplot = paste(outdir,"/PCA_PE_all_rep.png",sep="",collape=""); multisample_PCA(PE_df, sampleinfo_df, outplot); - + PCA_PE <- extractWidgetCode(outplot) + postscripts <- c(postscripts, PCA_PE$postscripts) # Replicate mode templist = mergeReplicates(TE_df,PE_df, sampleinfo_df, method); @@ -889,107 +1082,131 @@ # TE Boxplot outplot = paste(outdir,"/Box_TE_rep.png",sep="",collape=""); - 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', - "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE); temp_df_te_data = data.frame(TE_df[,1], log(TE_df[,2:length(TE_df)])); colnames(temp_df_te_data) = colnames(TE_df); multisample_boxplot(temp_df_te_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Transcript Abundance (log)"); - + lines <- extractWidgetCode(outplot) + #prescripts <- c(prescripts, lines$prescripts) + postscripts <- c(postscripts, lines$postscripts) + 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', + "<tr><td align=center>", '<img src="Box_TE_rep.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE); + # PE Boxplot outplot = paste(outdir,"/Box_PE_rep.png",sep="",collape=""); - cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE); temp_df_pe_data = data.frame(PE_df[,1], log(PE_df[,2:length(PE_df)])); colnames(temp_df_pe_data) = colnames(PE_df); multisample_boxplot(temp_df_pe_data, sampleinfo_df, outplot, "No", "Sample Groups", "Mean Protein Abundance (log)"); - + lines <- extractWidgetCode(outplot) + #prescripts <- c(prescripts, lines$prescripts) + postscripts <- c(postscripts, lines$postscripts) + cat("<td align=center>", '<img src="Box_PE_rep.png" width=500 height=500>', lines$widget_div, '</td></tr></table>\n', file = htmloutfile, append = TRUE); + #=============================================================================== # Calculating log fold change and running the "single" code part #=============================================================================== - + 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))); 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))); - - #=============================================================================== - # Treat missing values - #=============================================================================== - - TE_df[is.infinite(TE_df[,2]),2] = NA; - PE_df[is.infinite(PE_df[,2]),2] = NA; - TE_df[is.na(TE_df)] = 0; - PE_df[is.na(PE_df)] = 0; - - sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change")) - #=============================================================================== - # Find common samples - #=============================================================================== - - common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]); - TE_df = select(TE_df, 1, common_samples); - PE_df = select(PE_df, 1, common_samples); - sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples); - rownames(sampleinfo_df) = sampleinfo_df[,1]; - + + #=============================================================================== + # Treat missing values + #=============================================================================== + + TE_df[is.infinite(TE_df[,2]),2] = NA; + PE_df[is.infinite(PE_df[,2]),2] = NA; + TE_df[is.na(TE_df)] = 0; + PE_df[is.na(PE_df)] = 0; + + sampleinfo_df = data.frame("Sample"= c("LogFold"), "Group"=c("Fold_Change")) + #=============================================================================== + # Find common samples + #=============================================================================== + + common_samples = intersect(sampleinfo_df[,1], colnames(TE_df)[-1]) %>% intersect(., colnames(PE_df)[-1]); + TE_df = select(TE_df, 1, common_samples); + PE_df = select(PE_df, 1, common_samples); + sampleinfo_df = filter(sampleinfo_df, Sample %in% common_samples); + rownames(sampleinfo_df) = sampleinfo_df[,1]; + # TE Boxplot outplot = paste(outdir,"/Box_TE.png",sep="",collape=""); + multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)"); + lines <- extractWidgetCode(outplot) + postscripts <- c(postscripts, lines$postscripts) cat('<br><font color="#ff0000"><h3>Distribution (Box plot) of log fold change </h3></font>', file = htmloutfile, append = TRUE); cat('<table border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#7a0019"><th><font color=#ffcc33>Boxplot: Transcriptome data</font></th><th><font color=#ffcc33>Boxplot: Proteome data</font></th></tr>\n', - "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500></td>\n', file = htmloutfile, append = TRUE); - multisample_boxplot(TE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Transcript Abundance fold-change (log2)"); + "<tr><td align=center>", '<img src="Box_TE.png" width=500 height=500>', lines$widget_div, '</td>\n', file = htmloutfile, append = TRUE); # PE Boxplot outplot = paste(outdir,"/Box_PE.png",sep="",collape=""); - cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500></td></tr></table>\n', file = htmloutfile, append = TRUE); multisample_boxplot(PE_df, sampleinfo_df, outplot, "Yes", "Sample (log2(case/control))", "Protein Abundance fold-change(log2)"); + lines <- extractWidgetCode(outplot) + postscripts <- c(postscripts, lines$postscripts) + cat("<td align=center>", '<img src="Box_PE.png" width=500 height=500>', lines$widget_div,'</td></tr></table>\n', file = htmloutfile, append = TRUE); # Log Fold Data perform_Test_Volcano(TE_df_orig,PE_df_orig,TE_df, PE_df,sampleinfo_df_orig,method,correction_method,volc_with) - - + postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/TE_volcano.png",sep="",collapse=""))$postscripts) + postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_volcano.png",sep="",collapse=""))$postscripts) # Print PCA 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', - "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500></td>\n', - "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500></td></tr></table>\n', - file = htmloutfile, append = TRUE); + "<tr><td align=center>", '<img src="PCA_TE_all_rep.png" width=500 height=500>', PCA_TE$widget_div, '</td>\n', + "<td align=center>", '<img src="PCA_PE_all_rep.png" width=500 height=500>', PCA_PE$widget_div, '</td></tr></table>\n', + file = htmloutfile, append = TRUE); cat('<hr/><h2 id="corr_data"><font color=#ff0000>CORRELATION</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); + + PE_TE_data = data.frame(PE_df, TE_df); + colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance"); # TE PE scatter outplot = paste(outdir,"/TE_PE_scatter.png",sep="",collape=""); 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); - cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800></td>\n', file = htmloutfile, append = TRUE); - PE_TE_data = data.frame(PE_df, TE_df); - colnames(PE_TE_data) = c("PE_ID","PE_abundance","TE_ID","TE_abundance"); singlesample_scatter(PE_TE_data, outplot); - + lines <- extractWidgetCode(outplot); + postscripts <- c(postscripts, lines$postscripts); + cat("<tr><td align=center>", '<img src="TE_PE_scatter.png" width=800 height=800>', gsub('width:500px;height:500px', 'width:800px;height:800px' , lines$widget_div), + '</td>\n', file = htmloutfile, append = TRUE); + # TE PE Cor cat("<tr><td align=center>\n", file = htmloutfile, append = TRUE); singlesample_cor(PE_TE_data, htmloutfile, append=TRUE); 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', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat('</td></table>', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); cat('<hr/><h2 id="regression_data"><font color=#ff0000>REGRESSION ANALYSIS</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); # TE PE Regression singlesample_regression(PE_TE_data,htmloutfile, append=TRUE); + postscripts <- c(postscripts, c(extractWidgetCode(paste(outdir,"/PE_TE_lm_1.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_2.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_5.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/PE_TE_lm_cooksd.png",sep="",collapse=""))$postscripts, + extractWidgetCode(paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""))$postscripts, + gsub('data-for="html', 'data-for="secondhtml"', + extractWidgetCode(paste(outdir,"/TE_PE_scatter.png",sep="",collapse=""))$postscripts))); cat('<hr/><h2 id="cluster_data"><font color=#ff0000>CLUSTER ANALYSIS</font></h2>\n', - file = htmloutfile, append = TRUE); + file = htmloutfile, append = TRUE); #TE PE Heatmap singlesample_heatmap(PE_TE_data, htmloutfile, hm_nclust); + lines <- extractWidgetCode(paste(outdir,"/PE_TE_heatmap.png",sep="",collapse="")) + postscripts <- c(postscripts, lines$postscripts) + prescripts <- c(prescripts, lines$prescripts) #TE PE Clustering (kmeans) singlesample_kmeans(PE_TE_data, htmloutfile, nclust=as.numeric(numCluster)) - + postscripts <- c(postscripts, extractWidgetCode(paste(outdir,"/PE_TE_kmeans.png",sep="",collapse=""))$postscripts); } } cat("<h3>Go To:</h3>\n", @@ -1002,3 +1219,14 @@ "<br><a href=#>TOP</a>", file = htmloutfile, append = TRUE); cat("</body></html>\n", file = htmloutfile, append = TRUE); + + +#=============================================================================== +# Add masked-javascripts tags to HTML file in the head and end +#=============================================================================== + +htmllines <- readLines(htmloutfile) +htmllines[1] <- paste('<html>\n<head>\n', paste(prescripts, collapse='\n'), '\n</head>\n<body>') +cat(paste(htmllines, collapse='\n'), file = htmloutfile) +cat('\n', paste(postscripts, collapse='\n'), "\n", + "</body>\n</html>\n", file = htmloutfile, append = TRUE);
--- a/quantp.xml Fri Sep 14 12:22:31 2018 -0400 +++ b/quantp.xml Thu Dec 20 16:06:05 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="quantp" name="QuanTP" version="1.0.0"> +<tool id="quantp" name="QuanTP" version="1.1.0"> <description>Correlation between protein and transcript abundances</description> <requirements> <requirement type="package" version="1.10.4">r-data.table</requirement> @@ -6,6 +6,8 @@ <requirement type="package" version="0.7.6">r-dplyr</requirement> <requirement type="package" version="3.0.0">r-ggplot2</requirement> <requirement type="package" version="0.4.5">r-ggfortify</requirement> + <requirement type="package" version="4.8.0">r-plotly</requirement> + <requirement type="package" version="0.6.1.2">r-d3heatmap</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/quantp.r' @@ -108,6 +110,7 @@ <output name="html_file"> <assert_contents> <has_text text="SAMPLE DISTRIBUTION" /> + <has_text text="plotly" /> </assert_contents> </output> </test>