From ad09a294cc5426a13e711497bc6c5e83a567b11e Mon Sep 17 00:00:00 2001 From: Minamehr Date: Wed, 30 Oct 2024 12:12:40 +0100 Subject: [PATCH 1/3] update XML files and test-data --- tools/ampvis2/alpha_diversity.xml | 36 ++++++++++++++++-- .../AalborgWWTPs-alpha_diversity_plot.pdf | Bin 0 -> 5904 bytes .../AalborgWWTPs-alpha_diversity_plot2.pdf | Bin 0 -> 17316 bytes 3 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot.pdf create mode 100644 tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot2.pdf diff --git a/tools/ampvis2/alpha_diversity.xml b/tools/ampvis2/alpha_diversity.xml index 8bd2146ce30..6d4d07556bb 100644 --- a/tools/ampvis2/alpha_diversity.xml +++ b/tools/ampvis2/alpha_diversity.xml @@ -11,13 +11,32 @@ @@ -30,13 +49,19 @@ + + + + - + + + @@ -46,12 +71,15 @@ + + + @@ -62,6 +90,8 @@ + + Pdm6DuKb4b~m6j!GKWkygk{Cck1AsuglDmNX z)eR72<%>lCK{_x3425wAg3Ms<2s}`h6kq}T?*YYs9U#Y%qj3l{;m>f84hBsi-Qs~t 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zr8aqmrBO<=n!n30j!nDkruXg-p2BvjcGx7|`>mal9qu6uqg68fZlm5Doc|xFE%YB4 ziv9P_0cm?6yWiR#xO4ywTmR=t+uHuQy^Hlf0yap>+S1YjxM%=vAKD9LFNv?-3Tr&)^s2%XHz!-=*q>~g$~4N@8D`~VMzya{yj)Afczm4 z)BmEshT2=1Iz#Osz>kUOKn_+8_7=84Z>GOnc0nU|!~eQ;;WyU*2gLu}y71c)0BJzY zTz_A}fF=SahO((0FeJb__|2C;W#lX%ZWgZAU{h?+KfchRIr`t1GBRr03H@&xH$VUX9Sgq@&wq`@)!Eb Date: Wed, 30 Oct 2024 13:26:08 +0100 Subject: [PATCH 2/3] update XML files and test-data --- tools/ampvis2/alpha_diversity.xml | 23 ++++++++++++------ .../AalborgWWTPs-alpha_diversity_plot.pdf | Bin 5904 -> 0 bytes .../AalborgWWTPs-alpha_diversity_plot2.pdf | Bin 17316 -> 0 bytes 3 files changed, 15 insertions(+), 8 deletions(-) delete mode 100644 tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot.pdf delete mode 100644 tools/ampvis2/test-data/AalborgWWTPs-alpha_diversity_plot2.pdf diff --git a/tools/ampvis2/alpha_diversity.xml b/tools/ampvis2/alpha_diversity.xml index 6d4d07556bb..4bf978b156c 100644 --- a/tools/ampvis2/alpha_diversity.xml +++ b/tools/ampvis2/alpha_diversity.xml @@ -13,12 +13,12 @@ library(ampvis2, quietly = TRUE) d <- readRDS("$data") - a <- amp_alphadiv(d, + table <- amp_alphadiv(d, measure = c($m), richness = $richness @RAREFY_TOKEN@, ) - b <- amp_alphadiv(d, + plot <- amp_alphadiv(d, measure = c($m), richness = $richness @RAREFY_TOKEN@, @@ -26,9 +26,9 @@ plot_group_by = "$group_by", plot_scatter = $plot_scatter ) - write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) + write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) ggsave("$alphadiv_plot", - plot = b, + plot = plot, device = "$output_options.out_format" #if str($output_options.plot_width) != '' , width = $output_options.plot_width @@ -55,7 +55,7 @@ - + @@ -71,7 +71,11 @@ - + + + + + @@ -90,8 +94,11 @@ - - + + + + + Pdm6DuKb4b~m6j!GKWkygk{Cck1AsuglDmNX z)eR72<%>lCK{_x3425wAg3Ms<2s}`h6kq}T?*YYs9U#Y%qj3l{;m>f84hBsi-Qs~t zKaYbf5O@p`2Pfr|`$s-CLIDkBweBr0WoqSG^iX>m@nJ3UB*^fNUvFP? 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zr8aqmrBO<=n!n30j!nDkruXg-p2BvjcGx7|`>mal9qu6uqg68fZlm5Doc|xFE%YB4 ziv9P_0cm?6yWiR#xO4ywTmR=t+uHuQy^Hlf0yap>+S1YjxM%=vAKD9LFNv?-3Tr&)^s2%XHz!-=*q>~g$~4N@8D`~VMzya{yj)Afczm4 z)BmEshT2=1Iz#Osz>kUOKn_+8_7=84Z>GOnc0nU|!~eQ;;WyU*2gLu}y71c)0BJzY zTz_A}fF=SahO((0FeJb__|2C;W#lX%ZWgZAU{h?+KfchRIr`t1GBRr03H@&xH$VUX9Sgq@&wq`@)!Eb Date: Wed, 30 Oct 2024 13:55:38 +0100 Subject: [PATCH 3/3] update XML files --- tools/ampvis2/alpha_diversity.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/ampvis2/alpha_diversity.xml b/tools/ampvis2/alpha_diversity.xml index 4bf978b156c..d6940ae78fb 100644 --- a/tools/ampvis2/alpha_diversity.xml +++ b/tools/ampvis2/alpha_diversity.xml @@ -1,4 +1,4 @@ - + macros.xml