| Previous changeset 10:9a52306991b3 (2018-09-01) Next changeset 12:ddaf84e15d06 (2018-11-08) |
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Commit message:
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7 |
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modified:
w4mcorcov.xml w4mcorcov_calc.R w4mcorcov_lib.R w4mcorcov_util.R w4mcorcov_wrapper.R |
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| diff -r 9a52306991b3 -r ddcc33ff3205 w4mcorcov.xml --- a/w4mcorcov.xml Sat Sep 01 11:33:03 2018 -0400 +++ b/w4mcorcov.xml Wed Sep 05 22:31:21 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.14"> +<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.15"> <description>OPLS-DA Contrasts of Univariate Results</description> <macros> <xml name="paramPairSigFeatOnly"> @@ -419,20 +419,20 @@ <has_text text="vip4o" /> <!-- first matched line --> <has_text text="M349.2383T700" /> - <has_text text="-0.37867079" /> - <has_text text="-37.71066" /> - <has_text text="0.5246766" /> - <has_text text="0.0103341" /> + <has_text text="0.43361563" /> + <has_text text="37.76875778" /> + <has_text text="0.54672558" /> + <has_text text="0.3920409" /> <!-- second matched line --> <has_text text="M207.9308T206" /> - <has_text text="0.31570433" /> - <has_text text="5.86655640" /> - <has_text text="0.2111623" /> - <has_text text="0.0488654" /> + <has_text text="-0.3365475" /> + <has_text text="-6.337903" /> + <has_text text="0.270297" /> + <has_text text="0.037661" /> </assert_contents> </output> </test> - <!-- test #6 --> + <!-- test #6 - issue 6 --> <test> <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/> @@ -461,6 +461,32 @@ </assert_contents> </output> </test> + <!-- test #6 - issue 8 --> + <test> + <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> + <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/> + <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> + <param name="tesC" value="none"/> + <param name="facC" value="k._10"/> + <param name="labelFeatures" value="3"/> + <param name="levCSV" value="k_3,k-4"/> + <param name="matchingC" value="none"/> + <output name="contrast_corcov"> + <assert_contents> + <!-- column-labels line --> + <has_text text="featureID" /> + <has_text text="factorLevel1" /> + <has_text text="factorLevel2" /> + <has_text text="correlation" /> + <has_text text="covariance" /> + <has_text text="vip4p" /> + <has_text text="vip4o" /> + <!-- k1 rejected by levCSV, leaving only k_3 and k-4 --> + <not_has_text text="k1" /> + <not_has_text text="other" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ |
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| diff -r 9a52306991b3 -r ddcc33ff3205 w4mcorcov_calc.R --- a/w4mcorcov_calc.R Sat Sep 01 11:33:03 2018 -0400 +++ b/w4mcorcov_calc.R Wed Sep 05 22:31:21 2018 -0400 |
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| b'@@ -71,7 +71,9 @@\n # print("str(my_cor_vs_cov)")\n # str(my_cor_vs_cov)\n if (is.null(my_cor_vs_cov) || sum(!is.na(my_cor_vs_cov$tsv1$covariance)) < 2) {\n- x_progress("No cor_vs_cov data produced")\n+ if (is.null(cor_vs_cov_x)) {\n+ x_progress("No cor_vs_cov data produced")\n+ }\n plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")\n text(x=1, y=1, labels="too few covariance data")\n return(my_cor_vs_cov)\n@@ -561,7 +563,8 @@\n plot_action <- function(fctr_lvl_1, fctr_lvl_2) {\n progress_action(\n sprintf("calculating/plotting contrast of %s vs. %s"\n- , fctr_lvl_1, fctr_lvl_2))\n+ , fctr_lvl_1, fctr_lvl_2)\n+ )\n predictor <- sapply(\n X = chosen_facC\n , FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2\n@@ -569,7 +572,7 @@\n my_cor_cov <- do_detail_plot(\n x_dataMatrix = my_matrix\n , x_predictor = predictor\n- , x_is_match = is_match\n+ , x_is_match = TRUE\n , x_algorithm = algoC\n , x_prefix = if (pairSigFeatOnly) {\n "Significantly contrasting features"\n@@ -582,7 +585,7 @@\n , x_env = calc_env\n )\n if ( is.null(my_cor_cov) ) {\n- progress_action("NOTHING TO PLOT.")\n+ progress_action("NOTHING TO PLOT")\n } else {\n my_tsv <- my_cor_cov$tsv1\n my_tsv$mz <- mz_lookup(my_tsv$featureID)\n@@ -619,57 +622,72 @@\n fctr_lvl_2 <- col_match[3] # ^^ # Factor-level 2\n # only process this column if both factors are members of lvlCSV\n is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)\n- progress_action(\n- sprintf("calculating/plotting contrast of %s vs. %s"\n- , fctr_lvl_1, fctr_lvl_2))\n- # choose only samples with one of the two factors for this column\n- chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)\n- predictor <- smpl_metadata_facC[chosen_samples]\n- # extract only the significantly-varying features and the chosen samples\n- fully_significant <- 1 == vrbl_metadata[,vrbl_metadata_col] *\n- ( if (intersample_sig_col %in% colnames(vrbl_metadata)) {\n- vrbl_metadata[,intersample_sig_col]\n- } else {\n- 1\n- }\n+ if (is_match) {\n+ progress_action(\n+ sprintf("calculating/plotting contrast of %s vs. %s."\n+ , fctr_lvl_1, fctr_lvl_2\n+ )\n )\n- col_selector <- vrbl_metadata_names[\n- if ( pairSigFeatOnly ) fully_significant else overall_significant\n- ]\n- my_matrix <- tdm[ chosen_samples, col_selector, drop = FALSE ]\n- my_cor_cov <- do_detail_plot(\n- x_dataMatrix = my_matrix\n- , x_predictor = predictor\n- , x_is_match = is_match\n- , x_algorithm = algoC\n- , x_prefix = if (pairSigFeatOnly) {\n- "Significantly contrasting features"\n- } else {\n- "Significant features"\n- }\n- , x_show_labels = labelFeatures\n- , x_progress = progress_action\n- , x_crossval_i = min(7, length(chosen_samples))\n- , x_env = calc_env\n- )\n- if ( is.null(my_cor_cov) ) {\n- progress_action("NOTHING TO PLOT.")\n+ # choose only samples with one of the two factors for this column\n+ chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)\n+ predictor <- smpl_metadata_facC[chosen_samples]\n+ # extract only the significantly-varying features and the chosen samples\n+ fully_signi'..b'env = calc_env\n+ )\n+ if ( is.null(my_cor_cov) ) {\n+ progress_action("NOTHING TO PLOT...")\n+ } else {\n+ tsv <- my_cor_cov$tsv1\n+ tsv$mz <- mz_lookup(tsv$featureID)\n+ tsv$rt <- rt_lookup(tsv$featureID)\n+ corcov_tsv_action(tsv)\n+ did_plot <<- TRUE\n+ }\n } else {\n- tsv <- my_cor_cov$tsv1\n- tsv$mz <- mz_lookup(tsv$featureID)\n- tsv$rt <- rt_lookup(tsv$featureID)\n- corcov_tsv_action(tsv)\n- did_plot <<- TRUE\n }\n }\n "dummy" # need to return a value; otherwise combn fails with an error\n@@ -738,43 +762,56 @@\n fctr_lvl_1 <- x[1]\n fctr_lvl_2 <- x[2]\n chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)\n- progress_action(\n- sprintf("calculating/plotting contrast of %s vs. %s"\n- , fctr_lvl_1, fctr_lvl_2))\n if (length(unique(chosen_samples)) < 1) {\n- progress_action("NOTHING TO PLOT...")\n+ progress_action(\n+ sprintf("Skipping contrast of %s vs. %s. - There are no chosen samples."\n+ , fctr_lvl_1, fctr_lvl_2\n+ )\n+ )\n } else {\n chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])\n predictor <- chosen_facC\n my_matrix <- tdm[ chosen_samples, , drop = FALSE ]\n # only process this column if both factors are members of lvlCSV\n is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)\n- my_cor_cov <- do_detail_plot(\n- x_dataMatrix = my_matrix\n- , x_predictor = predictor\n- , x_is_match = is_match\n- , x_algorithm = algoC\n- , x_prefix = "Features"\n- , x_show_labels = labelFeatures\n- , x_progress = progress_action\n- , x_crossval_i = min(7, length(chosen_samples))\n- , x_env = calc_env\n- )\n- if ( is.null(my_cor_cov) ) {\n- progress_action("NOTHING TO PLOT")\n+ if (is_match) {\n+ progress_action(\n+ sprintf("Calculating/plotting contrast of %s vs. %s."\n+ , fctr_lvl_1, fctr_lvl_2)\n+ )\n+ my_cor_cov <- do_detail_plot(\n+ x_dataMatrix = my_matrix\n+ , x_predictor = predictor\n+ , x_is_match = is_match\n+ , x_algorithm = algoC\n+ , x_prefix = "Features"\n+ , x_show_labels = labelFeatures\n+ , x_progress = progress_action\n+ , x_crossval_i = min(7, length(chosen_samples))\n+ , x_env = calc_env\n+ )\n+ if ( is.null(my_cor_cov) ) {\n+ progress_action("NOTHING TO PLOT.....")\n+ } else {\n+ tsv <- my_cor_cov$tsv1\n+ tsv$mz <- mz_lookup(tsv$featureID)\n+ tsv$rt <- rt_lookup(tsv$featureID)\n+ corcov_tsv_action(tsv)\n+ did_plot <<- TRUE\n+ }\n } else {\n- tsv <- my_cor_cov$tsv1\n- tsv$mz <- mz_lookup(tsv$featureID)\n- tsv$rt <- rt_lookup(tsv$featureID)\n- corcov_tsv_action(tsv)\n- did_plot <<- TRUE\n+ progress_action(\n+ sprintf("Skipping contrast of %s vs. %s."\n+ , fctr_lvl_1, fctr_lvl_2\n+ )\n+ )\n }\n }\n "dummy" # need to return a value; otherwise combn fails with an error\n }\n )\n } else {\n- progress_action("NOTHING TO PLOT....")\n+ progress_action("NOTHING TO PLOT......")\n }\n }\n if (!did_plot) {\n' |
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| diff -r 9a52306991b3 -r ddcc33ff3205 w4mcorcov_lib.R --- a/w4mcorcov_lib.R Sat Sep 01 11:33:03 2018 -0400 +++ b/w4mcorcov_lib.R Wed Sep 05 22:31:21 2018 -0400 |
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| @@ -1,12 +1,3 @@ suppressMessages(library(batch)) -# suppressMessages(library(foreach)) suppressMessages(library(ropls)) suppressMessages(library(methods)) - -# cat("Installed packages:",stderr()) -# write.table((installed.packages(.Library, priority = "high"))[, c(1,3:5)], stderr()) -# cat("Loaded packages:",stderr()) -# write(.packages(), stderr()) - -print(sessionInfo()) - |
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| diff -r 9a52306991b3 -r ddcc33ff3205 w4mcorcov_util.R --- a/w4mcorcov_util.R Sat Sep 01 11:33:03 2018 -0400 +++ b/w4mcorcov_util.R Wed Sep 05 22:31:21 2018 -0400 |
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| @@ -21,10 +21,54 @@ return (retval) } +errorSink <- function(which_function, ...) { + var_args <- "..." + tryCatch( + var_args <<- (deparse(..., width.cutoff = 60)) + , error = function(e) {print(e$message)} + ) + if (var_args == "...") + return + # format error for logging + format_error <- function(e) { + sprintf( + "Error\n{ message: %s\n, arguments: %s\n}\n" + , e$message + , Reduce(f = paste, x = var_args) + ) + } + format_warning <- function(e) { + sprintf( + "Warning\n{ message: %s\n, arguments: %s\n}\n" + , e$message + , Reduce(f = paste, x = var_args) + ) + } + sink_number <- sink.number() + sink(stderr()) + tryCatch( + var_args <- (deparse(..., width.cutoff = 60)) + , expr = { + retval <- which_function(...) + } + , error = function(e) cat(format_error(e), file = stderr()) + , warning = function(w) cat(format_warning(w), file = stderr()) + ) + while (sink.number() > sink_number) { + sink() + } +} +errorPrint <- function(...) { + errorSink(which_function = print, ...) +} +errorCat <- function(...) { + errorSink(which_function = cat, ..., "\n") +} + # # pseudo-inverse - computational inverse of non-square matrix a # p.i <- function(a) { # solve(t(a) %*% a) %*% t(a) # } - +# vim: sw=2 ts=2 et ai : |
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| diff -r 9a52306991b3 -r ddcc33ff3205 w4mcorcov_wrapper.R --- a/w4mcorcov_wrapper.R Sat Sep 01 11:33:03 2018 -0400 +++ b/w4mcorcov_wrapper.R Wed Sep 05 22:31:21 2018 -0400 |
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| @@ -72,7 +72,12 @@ # MAIN # ######## +errorPrint(sessionInfo()) + argVc <- unlist(parseCommandArgs(evaluate=FALSE)) +errorCat("\n\n---\n\nArguments that were passed to R are as follows:\n") +errorPrint(argVc) + my_env <- new.env() ##------------------------------ |