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PR to fix krona plots #51

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merged 4 commits into from
Aug 26, 2024
Merged

PR to fix krona plots #51

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6e8aebe
add metadata as input when samplesheet
Aug 23, 2024
5d20fa9
deleted param sample_label
daulet-a Aug 26, 2024
e4218e7
fixed the Sample column name
daulet-a Aug 26, 2024
783b288
updated ignore
daulet-a Aug 26, 2024
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
zamp.egg-info/
zamp/__pycache__
zamp/ressources/
zamp/ressources/
build/
1 change: 1 addition & 0 deletions zamp/Snakefile
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Expand Up @@ -66,6 +66,7 @@ if os.path.isdir(INPUT) and METADATA:
SAMPLES.set_index("sample", inplace=True)
elif os.path.isfile(INPUT) and not METADATA:
SAMPLES = pd.read_csv(INPUT, sep="\t", index_col="sample")
METADATA = INPUT


# Add read pairing
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1 change: 0 additions & 1 deletion zamp/rules/5_visualization/General_plotting.rules
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Expand Up @@ -216,7 +216,6 @@ rule KRONA_plots:
params:
grouping_column=lambda wildcards: wildcards.grouping_column,
grouping_col_value=lambda wildcards: wildcards.grouping_col_value,
sample_label="sample",
log:
os.path.join(
dir.logs,
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7 changes: 2 additions & 5 deletions zamp/rules/5_visualization/scripts/KRONA_plots.R
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Expand Up @@ -19,7 +19,6 @@
output_folder <- (dirname(output_folder)[1])

## Parameters
sample_label <- snakemake@params[["sample"]]
grouping_column <- snakemake@params[["grouping_column"]]
grouping_filter_column_value <- snakemake@params[["grouping_col_value"]]

Expand All @@ -30,10 +29,8 @@
melted_dataframe<- read.csv(file.path(phyloseq_melted_table), header = TRUE, sep = "\t")

## Create KRONA
df <- filter(melted_dataframe, melted_dataframe[[grouping_column]] == grouping_filter_column_value)
df <- filter(df, df[["Abundance"]] != 0)

df <- df[, c("Abundance", sample_label, "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species", "OTU")]
df <- subset(melted_dataframe, sample_group == grouping_filter_column_value & Abundance !=0)
df <- df[, c("Abundance", "Sample", "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species", "OTU")]
df <- as.data.frame(unclass(df))
df[, 2] <- gsub(" |\\(|\\)", "", df[, 2])
df[, 2] <- as.factor(df[, 2])
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