| Previous changeset 1:08678c931f5d (2022-10-28) Next changeset 3:dda27b9273a8 (2023-01-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254 |
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modified:
macros.xml mqppep_anova_script.Rmd |
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added:
overview_flowchart.dia overview_flowchart.pdf |
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| diff -r 08678c931f5d -r 2336fbff8866 macros.xml --- a/macros.xml Fri Oct 28 18:27:21 2022 +0000 +++ b/macros.xml Mon Dec 12 22:01:09 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.15</token> + <token name="@TOOL_VERSION@">0.1.16</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -41,7 +41,7 @@ </requirements> <!-- I specified the versions above because it takes a VERY long time to search for package versions when they are not omitted; also, - locking version numbers might lead to more-reproducible behavior. + locking version numbers might lead to more-reproducible behavior. --> </xml> </macros> |
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| diff -r 08678c931f5d -r 2336fbff8866 mqppep_anova_script.Rmd --- a/mqppep_anova_script.Rmd Fri Oct 28 18:27:21 2022 +0000 +++ b/mqppep_anova_script.Rmd Mon Dec 12 22:01:09 2022 +0000 |
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| @@ -6,7 +6,7 @@ - "Art Eschenlauer^[ORCiD 0000-0002-2882-0508, University of Minnesota: Minneapolis, Minnesota, US]" date: - "May 28, 2018" -- "; revised June 23, 2022" +- "; revised December 7, 2022" lot: true output: pdf_document: @@ -97,13 +97,14 @@ kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" # should debugging trace messages be printed? showEnrichedSubstrates: FALSE - # should debugging nb/nbe messages be printed? printNBMsgs: FALSE + # showld row-scaling be applied to heatmaps: "none" or "row" + defaultHeatMapRowScaling: "none" # should debugging trace messages be printed? printTraceMsgs: FALSE # when debugging files are needed, set debugFileBasePath to the path - # to the directory where they should be writtn + # to the directory where they should be written debugFileBasePath: !r if (TRUE) NULL else "test-data" --- @@ -556,6 +557,16 @@ } ) +g_default_heatmap_row_scaling <- + params$defaultHeatMapRowScaling +if ( + !is.character(g_default_heatmap_row_scaling) || + !(g_default_heatmap_row_scaling %in% c("row", "none")) + ) { + cat("invalid defaultHeatMapRowScaling (must be 'row' or 'none')") + knitr::knit_exit() +} + # intensityHeatmapRows: 50 # TODO Validate >> 0 < 75 g_intensity_hm_rows <- params$intensityHeatmapRows @@ -2287,7 +2298,16 @@ my_limit <- g_intensity_hm_rows my_row_cex_scale <- master_cex * 150 / nrow_x + #ACE row cex shrink hack begin + my_row_cex_scale <- master_cex * 150 / max(nrow_x, ncol_x) + #ACE row cex shrink hack end + my_col_cex_scale <- 3.0 + #ACE col cex shrink hack begin + if (ncol_x > 40) + my_col_cex_scale <- 3.0 * 40 / ncol_x + #ACE col cex shrink hack end + my_asterisk_scale <- 0.4 * my_row_cex_scale my_row_warp <- 1 my_note_warp <- 2 @@ -2606,6 +2626,8 @@ margins = NULL, # optional margins (bottom, right) cellnote = NULL, # optional matrix of character; dim = dim(m) adj = 0.5, # adjust text: 0 left, 0.5 middle, 1 right + row_scaling = # should row-scaling be applied if possible? + g_default_heatmap_row_scaling, ... # passthru to hm2plus or heatmap.2 ) { use_heatmap_1 <- FALSE @@ -2780,11 +2802,11 @@ } # invoke hm_call inner function - if (sum(rowSums(!is.na(m_hm)) < 2)) + if (row_scaling != "row" || sum(rowSums(!is.na(m_hm)) < 2)) hm_call( m_hm, "none", - "log(intensities), unscaled, unimputed, and unnormalized" + "log(intensities), unimputed, and unnormalized" ) else hm_call( @@ -2802,10 +2824,7 @@ hm_call( m_hm, "none", - paste( - "log(intensities), unscaled,", - "zero-imputed, unnormalized" - ) + "log(intensities), zero-imputed, unnormalized" ) else cat("\nThere are too few peptides to produce a heatmap.\n") @@ -3715,12 +3734,8 @@ imp_smry_rejected_after <- sum(!good_rows) imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ])) -# From ?`%in%`, %in% is currently defined as function(x, table) match(x, table, nomatch = 0) > 0 - -sink(stderr()) -print("`%in%`:") -print(`%in%`) -sink() +# From ?`%in%`: +# %in% is currently defined as function(x, table) match(x, table, nomatch = 0) > 0 stock_in <- names(good_rows) %in% @@ -5094,33 +5109,38 @@ one_way_f = one_way_two_categories, # anova_func arg3 simplify = TRUE # TRUE is the default for simplify ) - contrast_data_adj_p_values <- p.adjust( - p = p_value_data_contrast_ps, - method = "fdr", - n = length(p_value_data_contrast_ps) # this is the default, length(p) - ) - # - compute the fold-change - contrast_p_df <- - data.frame( - contrast = contrast, - phosphopep = contrast_cast$phosphopep, - p_value_raw = p_value_data_contrast_ps, - p_value_adj = contrast_data_adj_p_values + + if (!is.null(p_value_data_contrast_ps)) { + contrast_data_adj_p_values <- + p.adjust( + p = p_value_data_contrast_ps, + method = "fdr", + n = length(p_value_data_contrast_ps) # this is the default, length(p) + ) + + # - compute the fold-change + contrast_p_df <- + data.frame( + contrast = contrast, + phosphopep = contrast_cast$phosphopep, + p_value_raw = p_value_data_contrast_ps, + p_value_adj = contrast_data_adj_p_values + ) + db_write_table_overwrite <- (contrast < 2) + db_write_table_append <- !db_write_table_overwrite + RSQLite::dbWriteTable( + conn = db, + name = "contrast_ppep_p_val", + value = contrast_p_df, + append = db_write_table_append + ) + # Create UK for insert + ddl_exec(db, " + CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx + ON contrast_ppep_p_val(phosphopep, contrast); + " ) - db_write_table_overwrite <- (contrast < 2) - db_write_table_append <- !db_write_table_overwrite - RSQLite::dbWriteTable( - conn = db, - name = "contrast_ppep_p_val", - value = contrast_p_df, - append = db_write_table_append - ) - # Create UK for insert - ddl_exec(db, " - CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx - ON contrast_ppep_p_val(phosphopep, contrast); - " - ) + } } # Perhaps this could be done more elegantly using unique keys # or creating the tables before saving data to them, but this @@ -6095,7 +6115,8 @@ suppress_row_dendrogram = FALSE, master_cex = 0.35, sepcolor = "black", - colsep = sample_colsep + colsep = sample_colsep, + row_scaling = "none" ) if (number_of_peptides_found > 1) { |
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