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library(MetaboAnalystR)
rm(list = ls())
mSet<-InitDataObjects("conc", "stat", FALSE); mSet<-Read.TextData(mSet, "https://rest.xialab.ca/api/download/metaboanalyst/human_cachexia.csv", "rowu", "disc"); mSet<-SanityCheckData(mSet); mSet<-ReplaceMin(mSet); mSet<-PreparePrenormData(mSet); mSet<-Normalization(mSet, "NULL", "LogNorm", "MeanCenter", "S10T0", ratio=FALSE, ratioNum=20); mSet<-PlotNormSummary(mSet, "norm_0_", format ="png", dpi=72, width=NA); mSet<-PlotSampleNormSummary(mSet, "snorm_0_", format = "png", dpi=72, width=NA);
mSet<-FC.Anal(mSet, 2.0, 0, FALSE) mSet<-PlotFC(mSet, "fc_0_", "png", 72, width=NA)
mSet<-Ttests.Anal(mSet, nonpar=F, threshp=0.05, paired=FALSE, equal.var=TRUE, "fdr", TRUE)
mSet<-PlotTT(mSet, imgName = "tt_0_", format = "png", dpi = 72, width=NA)
mSet<-Volcano.Anal(mSet, FALSE, 2.0, 0, F, 0.1, TRUE, "raw")
mSet<-PlotVolcano(mSet, "volcano_0_", 1, 0, format ="png", dpi=72, width=NA)
mSet<-PlotCorrHeatMap(mSet, "corr_0_", "png", 72, width=NA, "col", "pearson", "bwm", "overview", F, F, 0.0)
code is above, R version is 4.4.1. It raised an error: Error in if (fix.col) {: argument can't be used as a logical value
it seems that code 'if(fix.col){ p <- iheatmap(corr.mat, name = "CorrelationCoefficient", colors = colors,zmin=-1,zmid=0, zmax=1, colorbar_grid = setup_colorbar_grid(y_start = 0.85)) %>% add_row_labels(size = 0.2, side = "right",font = list(size = fz))%>% add_col_labels(size = 0.2, font = list(size = fz))
}else{ p <- iheatmap(corr.mat, name = "CorrelationCoefficient" , colors = colors,zmin=min(corr.mat),zmid=mean(min(corr.mat),max(corr.mat)), zmax=max(corr.mat), colorbar_grid = setup_colorbar_grid(y_start = 0.85) ) %>% add_row_labels(size = 0.2, side = "right",font = list(size = fz))%>% add_col_labels(size = 0.2,font = list(size = fz) ) }' can not recognize 'TRUE' and 'FALSE'?
The text was updated successfully, but these errors were encountered:
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Load MetaboAnalystR
library(MetaboAnalystR)
Clean global environment
rm(list = ls())
mSet<-InitDataObjects("conc", "stat", FALSE);
mSet<-Read.TextData(mSet, "https://rest.xialab.ca/api/download/metaboanalyst/human_cachexia.csv", "rowu", "disc");
mSet<-SanityCheckData(mSet);
mSet<-ReplaceMin(mSet);
mSet<-PreparePrenormData(mSet);
mSet<-Normalization(mSet, "NULL", "LogNorm", "MeanCenter", "S10T0", ratio=FALSE, ratioNum=20);
mSet<-PlotNormSummary(mSet, "norm_0_", format ="png", dpi=72, width=NA);
mSet<-PlotSampleNormSummary(mSet, "snorm_0_", format = "png", dpi=72, width=NA);
Perform fold-change analysis on uploaded data, unpaired
mSet<-FC.Anal(mSet, 2.0, 0, FALSE)
mSet<-PlotFC(mSet, "fc_0_", "png", 72, width=NA)
Perform T-test (parametric)
mSet<-Ttests.Anal(mSet, nonpar=F, threshp=0.05, paired=FALSE, equal.var=TRUE, "fdr", TRUE)
Plot of the T-test results
mSet<-PlotTT(mSet, imgName = "tt_0_", format = "png", dpi = 72, width=NA)
Perform the volcano analysis
mSet<-Volcano.Anal(mSet, FALSE, 2.0, 0, F, 0.1, TRUE, "raw")
Create the volcano plot
mSet<-PlotVolcano(mSet, "volcano_0_", 1, 0, format ="png", dpi=72, width=NA)
OPTION 1 - Heatmap specifying pearson distance and an overview
mSet<-PlotCorrHeatMap(mSet, "corr_0_", "png", 72, width=NA, "col", "pearson", "bwm", "overview", F, F, 0.0)
code is above, R version is 4.4.1.
It raised an error: Error in if (fix.col) {: argument can't be used as a logical value
it seems that code 'if(fix.col){
p <- iheatmap(corr.mat, name = "Correlation
Coefficient",
colors = colors,zmin=-1,zmid=0, zmax=1,
colorbar_grid = setup_colorbar_grid(y_start = 0.85)) %>%
add_row_labels(size = 0.2, side = "right",font = list(size = fz))%>%
add_col_labels(size = 0.2, font = list(size = fz))
}else{
p <- iheatmap(corr.mat, name = "Correlation
Coefficient" ,
colors = colors,zmin=min(corr.mat),zmid=mean(min(corr.mat),max(corr.mat)), zmax=max(corr.mat),
colorbar_grid = setup_colorbar_grid(y_start = 0.85) ) %>%
add_row_labels(size = 0.2, side = "right",font = list(size = fz))%>%
add_col_labels(size = 0.2,font = list(size = fz) )
}' can not recognize 'TRUE' and 'FALSE'?
The text was updated successfully, but these errors were encountered: