Mercurial > repos > eschen42 > w4mcorcov
comparison w4mcorcov_wrapper.R @ 6:7bd523ca1f9a draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
author | eschen42 |
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date | Wed, 18 Jul 2018 12:35:55 -0400 |
parents | 50f60f94c034 |
children | 342570ad880c |
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5:50f60f94c034 | 6:7bd523ca1f9a |
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31 | 31 |
32 ## log file | 32 ## log file |
33 ##--------- | 33 ##--------- |
34 | 34 |
35 my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))} | 35 my_log <- function(x, ...) { cat(paste(iso8601.znow(), " ", x, ..., nl, sep=""))} |
36 my_fatal <- function(x, ...) { | 36 my_fatal <- function(x, ...) { |
37 my_log("ERROR: ", x, ...) | 37 my_log("ERROR: ", x, ...) |
38 quit(save = "no", status = 11, runLast = TRUE) | 38 quit(save = "no", status = 11, runLast = TRUE) |
39 } | 39 } |
40 | 40 |
41 my_log("Start of the '", modNamC, "' Galaxy module call: ") | 41 my_log("Start of the '", modNamC, "' Galaxy module call: ") |
70 my_env$facC <- as.character(argVc["facC"]) | 70 my_env$facC <- as.character(argVc["facC"]) |
71 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) | 71 my_env$pairSigFeatOnly <- as.logical(argVc["pairSigFeatOnly"]) |
72 my_env$levCSV <- as.character(argVc["levCSV"]) | 72 my_env$levCSV <- as.character(argVc["levCSV"]) |
73 my_env$matchingC <- as.character(argVc["matchingC"]) | 73 my_env$matchingC <- as.character(argVc["matchingC"]) |
74 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' | 74 my_env$labelFeatures <- as.character(argVc["labelFeatures"]) # number of features to label at each extreme of the loadings or 'ALL' |
75 my_env$cplot_o <- as.logical(argVc["cplot_o"]) # TRUE if orthogonal C-plot is requested | |
76 my_env$cplot_p <- as.logical(argVc["cplot_p"]) # TRUE if parallel C-plot is requested | |
77 my_env$cplot_y <- as.character(argVc["cplot_y"]) # Choice of covariance/correlation for Y-axis on C-plot | |
75 | 78 |
76 label_features <- my_env$labelFeatures | 79 label_features <- my_env$labelFeatures |
77 labelfeatures_check <- TRUE | 80 labelfeatures_check <- TRUE |
78 if ( is.na(label_features) ) { | 81 if ( is.na(label_features) ) { |
79 labelfeatures_check <- FALSE | 82 labelfeatures_check <- FALSE |
126 # receiver for result of the call to corcov_calc | 129 # receiver for result of the call to corcov_calc |
127 my_result <- NULL | 130 my_result <- NULL |
128 | 131 |
129 # compute and plot the correlation_vs_covariance details plot | 132 # compute and plot the correlation_vs_covariance details plot |
130 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source. | 133 # The parameter settings here are generally taken from bioconductor ropls::plot.opls source. |
131 marVn <- c(4.6, 4.1, 2.6, 1.6) | 134 if ( my_env$cplot_p || my_env$cplot_o ) { |
132 old_par <- par( | 135 old_par <- par( |
133 font = 2 # bold font face | 136 font = 2 # bold font face |
134 , font.axis = 2 # bold font face for axis | 137 , font.axis = 2 # bold font face for axis |
135 , font.lab = 2 # bold font face for x and y labels | 138 , font.lab = 2 # bold font face for x and y labels |
136 , lwd = 2 # line-width - interpretation is device spcific | 139 , lwd = 2 # line-width - interpretation is device spcific |
137 , mar = marVn # margins | 140 , pch = 18 # black diamond plot-character, see help for graphics::points |
138 , pch = 18 # black diamond plot-character, see help for graphics::points | 141 , pty = "m" # do not force plots to be square |
139 # , mfrow = c(2,2) # two rows by two columns | 142 , no.readonly = TRUE # only save writable parameters |
140 , pty = "s" # force plots to be square | 143 ) |
141 ) | 144 pdf_height <- 12 |
145 pdf_width <- 8 | |
146 my_layout <- function() { | |
147 # lay out 2 columns by 3 rows with extra width at the margin of individual plots | |
148 layout( | |
149 matrix( | |
150 # blank row plot 1 & 2 blank row plot 3 & 4 blank row plot 5 & 6 blank row | |
151 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0, 0,5,0,6,0, 0,0,0,0,0) | |
152 , nrow = 7 | |
153 , ncol = 5 | |
154 , byrow = TRUE | |
155 ) | |
156 # slim columns 1, 3, and 5 | |
157 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1) | |
158 # slim rows 1, 3, 5, and 7 | |
159 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1, 0.9, 0.1) | |
160 ) | |
161 } | |
162 } else { | |
163 old_par <- par( | |
164 font = 2 # bold font face | |
165 , font.axis = 2 # bold font face for axis | |
166 , font.lab = 2 # bold font face for x and y labels | |
167 , lwd = 2 # line-width - interpretation is device spcific | |
168 , pch = 18 # black diamond plot-character, see help for graphics::points | |
169 , pty = "m" # do not force plots to be square | |
170 , no.readonly = TRUE # only save writable parameters | |
171 ) | |
172 pdf_height <- 8 | |
173 pdf_width <- 8 | |
174 my_layout <- function() { | |
175 # lay out 2 columns by 2 rows with extra width at the margin of individual plots | |
176 layout( | |
177 matrix( | |
178 # blank row plot 1 & 2 blank row plot 3 & 4 blank row | |
179 c(0,0,0,0,0, 0,1,0,2,0, 0,0,0,0,0, 0,3,0,4,0, 0,0,0,0,0) | |
180 , nrow = 5 | |
181 , ncol = 5 | |
182 , byrow = TRUE | |
183 ) | |
184 # slim columns 1, 3, and 5 | |
185 , widths = c(0.1, 0.9, 0.1, 0.9, 0.1) | |
186 # slim rows 1, 3, and 5 | |
187 , heights = c(0.1, 0.9, 0.1, 0.9, 0.1) | |
188 ) | |
189 } | |
190 } | |
142 plot2pdf( | 191 plot2pdf( |
143 file.name = my_env$contrast_detail | 192 file.name = my_env$contrast_detail |
144 , width = 8 | 193 , width = pdf_width |
145 , height = 8 | 194 , height = pdf_height |
146 , plot.function = function() { | 195 , plot.function = function() { |
147 # plot layout four plots per page | 196 # plot layout four or six plots per page |
148 layout(matrix(1:4, byrow = TRUE, nrow = 2)) | 197 my_layout() |
149 my_result <<- corcov_calc( | 198 my_result <<- corcov_calc( |
150 calc_env = my_env | 199 calc_env = my_env |
151 , failure_action = my_fatal | 200 , failure_action = my_fatal |
152 , progress_action = my_log | 201 , progress_action = my_log |
153 , corcov_tsv_action = corcov_tsv_action | 202 , corcov_tsv_action = corcov_tsv_action |
154 , salience_tsv_action = salience_tsv_action | 203 , salience_tsv_action = salience_tsv_action |
155 ) | 204 ) |
156 } | 205 } |
157 ) | 206 ) |
158 par(old_par) | 207 par(old_par) |
159 | 208 |
160 my_log( "-------------------------- Finished data processing --------------------------") | 209 my_log( "-------------------------- Finished data processing --------------------------") |
161 } | 210 } |
162 | 211 |
163 my_log( "End of the '", modNamC, "' Galaxy module call") | 212 my_log( "End of the '", modNamC, "' Galaxy module call") |
164 | 213 |