ChiLiubio
commented
6 months ago Hi Venkat,
The easiest way is to use order_x parameter in plot_bar function. Let me show an example.
library(microeco)
library(ggplot2)
t1 <- trans_abund$new(dataset = dataset, taxrank = "Phylum", ntaxa = 7)
t1$plot_bar(facet = c("Group", "Type"), xtext_angle = 30, xtext_size = 8)
ggsave('test1.jpeg', units="in", width = 20, height = 7)
t1$plot_bar(facet = c("Group", "Type"), order_x = rev(rownames(dataset$sample_table)), xtext_angle = 30, xtext_size = 8)
ggsave('test2.jpeg', units="in", width = 20, height = 7)We can see, in figure test2, the order of x axis has a reverse direction within each fixed facet. Another way is to assign factor levels in t1$data_abund$Sample.
The reason that you failed to make meco_dataset$sample_table$SampleID to be factors is the name of x axis comes from converted rownames of sample_table (i.e., t1$data_abund$Sample), not the SampleID of sample_table. The design reason is many users donot have a habit to add a SampleID column in the sample_table. Thus I have to add a parameter to control this.
Best, Chi
srisvs33
Hi @ChiLiubio
I was able to reorder the groups according to the example given in the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#group-order). However, I need to reorder sample IDs (sample names) in a barplot.
Here is the code that I have used for .. However, it did'n change as per my given order. Any suggestions on how to change the sample order asper custom list.
Thank you very much Venkat
Code
meco_dataset$sample_table$Sample_type %<>% factor(., levels = c("PA", "FL"))
str(dataset$sample_table)
meco_dataset$sample_table$Hydrography %<>% factor(., levels = c("TPDW", "FZ","AW"))
str(dataset$sample_table)
meco_dataset$sample_table$SampleID%<>% factor(., levels = c("3A","4A","11A","12A","15A","16A","19A","20A","27A","28A","31A","32A","35A","36A","39A","40A","43A","44A","47A","48A","51A","52A","55A","56A","59A","60A","3B","4B","11B","12B","15B","16B","19B","20B","23B","24B","27B","28B","31B","32B","35B","36B","39B","40B","43B","44B","47B","48B","51B","52B","55B","56B","59B","60B")) str(dataset$sample_table)
t1 <- trans_abund$new(dataset = meco_dataset, taxrank = "Phylum", ntaxa = 7)
PC53 = t1$plot_bar(color_values = paletteer_d("ggsci::category10_d3"),others_color = "grey70", facet = c("Sample_type", "Hydrography"), xtext_keep = TRUE, legend_text_italic = TRUE, barwidth = 0.8) +theme_classic()
print(PC53) ggsave('test4.jpeg', units="in", width=20, height=7, dpi=600)